Biology subjects

Thomas, J. H.

Publications and source records attributed to Thomas, J. H..

9 recordsLinked to original sources

bioRxiv2024

The role of local and long-range stresses in cephalic furrow formation in the Drosophila melanogaster embryo

Cephalic furrow (CF) is a transient epithelial invagination that forms during early gastrulation in the Drosophila melanogaster embryo. The initial stage of cephalic furrow formation (CFF) involves a shortening of initiator cells, generation of a localized asymmetric protrusion inwards, and then subsequent descent of cells into the yolk sac area. We present an analysis of how local forces associated with cell-membrane tensions and cell pressures interact with the long-range tensile stress developing along the furrow to generate the invagination. We propose two numerical models which capture different aspects of CFF. First, we formulate a force-center model of CF to show how the spatiotemporal heterogeneity of initiator-cell activation observed in vivo is a result of tensile-stress-feedback-based intercellular coordination. We also argue that this kind of mechanical stress-based activation mechanism likely contributes to robustness of the overall process. Second, we use our multi-node lateral vertex model to analyze the mechanical dynamics of the anterior-posterior cross-section of CF. This approach allows us to quantify the balance between cortical membrane tension forces, cellular pressures, and the inward force produced by the tension along the curved apical surface of the embryo. Comparing our simulations to experimental images, we discuss the crucial and indispensable role of the tension-induced inward force, especially during the initial stages of CFF where the localized asymmetric protrusion is formed. We argue that without this inward force the initial descent of the initiator cells into the furrow would not be possible, and that at later stages the inward force provides redundancy to this process and thus aids CFF robustness.

biophysics↗

bioRxiv2023

The mechanics of cephalic furrow formation in the Drosophila embryo

Cephalic furrow formation (CFF) is a major morphogenetic movement during gastrulation in Drosophila melanogaster embryos that gives rise to a deep, transitory epithelial invagination. Recent studies have identified the individual cell shape changes that drive the initiation and progression phases of CFF; however, the underlying mechanics of these changes are not yet well understood. During the progression phase, the furrow deepens as columnar cells from both the anterior and posterior directions fold inwards rotating by 90{degrees}. To analyze the mechanics of this process, we have developed an advanced 2D vertex model, which introduces multi-node representation of cellular membranes and allows us to capture the membrane curvature associated with pressure variation. Our investigations reveal some key mechanical features of CFF. As cells begin to roll over the cephalic furrow cleft, they become wedge-shaped as their apical cortices and overlying membranes expand, lateral cortices and overlying membranes release tension, internal pressures drop, and basal cortices and membranes contract. Cells then reverse the process by shortening apical cortices and membranes, increasing lateral tension, and causing internal pressures to rise. Since the basal membranes expand, the cells recover a rotated columnar shape at the end of this process. Interestingly, our findings indicate that the basal membranes may be passively reactive throughout the progression phase. We also find that the smooth rolling of cells over the cephalic furrow cleft necessitates that internalized cells provide a solid base through high membrane tensions and internal pressure levels, which allows transmission of tensile force that pulls new cells into the furrow. These results lead us to suggest that CFF may help establish a baseline tension across the apical surface of the embryo that would facilitate cellular coordination of other morphogenetic movements via mechanical stress feedback mechanisms. SIGNIFICANCEMechanical forces and stress feedback are essential for the development of morphology and structure in the embryo. Although great progress has been made in understanding the genetic control of patterning and cell fate, mechanical stress contributions are not as well understood. Mechanical analyses of the apical constrictions initiating ventral furrow formation and subsequent invagination dynamics in Drosophila have shed considerable light on these processes; however, ventral furrow formation is only one of many morphogenetic movements. Cephalic furrow formation occurs simultaneously with ventral furrow formation, but its cell shape changes and invagination dynamics are radically different. This study shows that mechanical forces and feedback operating in cephalic furrow formation also differ considerably from those in ventral furrow, demonstrating a potentially wide array of mechanical processes in morphogenesis.

biophysics↗

bioRxiv2021

A network model of glymphatic flow under different experimentally-motivated parametric scenarios

Rapidly growing evidence demonstrates that flow of cerebrospinal fluid (CSF) through perivascular spaces (PVSs) - annular channels surrounding vasculature in the brain - is a critically-important component of neurophysiology. CSF inflow contributes during physiological conditions to clearance of metabolic waste and in pathological situations to edema formation. However, brain-wide imaging methods cannot resolve PVSs, and high-resolution methods cannot access deep tissue or be applied to human subjects, so theoretical models provide essential insight. We model this CSF pathway as a network of hydraulic resistances, built from published parameters. A few parameters have very wide uncertainties, so we focus on the estimated limits of their feasible ranges by analyzing different parametric scenarios. We identify low-resistance PVSs and high-resistance parenchyma (brain tissue) as the scenario that best explains experimental observations. Our results point to the most important parameters that should be measured in future experiments. Extensions of our modeling may help predict stroke severity or lead to neurological disease treatments and drug delivery methods.

neuroscience↗

bioRxiv2020

Bulk flow of cerebrospinal fluid observed in periarterial spaces is not an artifact of injection

Cerebrospinal fluid (CSF) flowing through periarterial spaces is integral to the brains mechanism for clearing metabolic waste products. Experiments that track tracer particles injected into the cisterna magna of mouse brains have shown evidence of pulsatile CSF flow in pial periarterial spaces, with a bulk flow in the same direction as blood flow. However, the driving mechanism remains elusive. Several studies have suggested that the bulk flow might be an artifact, driven by the injection itself. Here, we address this hypothesis with new in vivo experiments where tracer particles are injected into the cisterna magna using a dual-syringe system, with simultaneous injection and withdrawal of equal amounts of fluid. This method produces no net increase in CSF volume and no significant increase in intracranial pressure. Yet, particle-tracking reveals flows in the pial periarterial spaces that are completely consistent with the flows observed in earlier experiments with single-syringe injection.

neuroscience↗

bioRxiv2020

Genome-Wide Search for Candidate Drivers of Adaptation Reveals Genes Enriched for Shifts in Purifying Selection (SPurS)

An open question in comparative evolutionary genomics is whether or not certain loci are the primary drivers of divergence between taxonomic lineages or species groups. Alternatively, genetic drivers of species divergence may be evenly distributed across the genome. The increasing availability of genome sequences from diverse taxa has enabled the development of novel methods to address this question. Genomes of many highly diverged species may now be compared in order to tease apart genetic differences that drive adaptive or functional divergence, and genetic differences that are observed by chance and are not causally linked to traits that differ between species or lineages. In order to test the hypothesis that a particular subset of loci or genes is responsible for driving adaptive changes between mammals and non-mammals, we developed a novel comparative approach to identify sites that are highly conserved within lineages or species groups and diverge between them. Loci with a high concentration of these sites may be called Shifts in Purifying Selection (SPurS) because a change has occurred between two groups of species at some point in the past, and the shift is conserved (via purifying selection) over a long period of time. Evaluating 7484 orthologous gene copies from 76 vertebrate species, we developed an empirical distribution of SPurS across the genome between Synapsida (placental and non-placental mammals) and Sauropsida (birds, crocodilians, squamates, and turtles), and compared this distribution to the expected null distribution of SPurS using matched simulated data. We then identified a subset of genes that is enriched for SPurS, relative to the full set of genes and to their matched simulated alignments. These SPurS-enriched genes are thus likely candidate drivers of functional divergence or adaptation between the mammalian and non-mammalian species groups in our analysis. Investigators seeking to identify genetic drivers of inter-species evolution may find this method useful, and we provide a web-based software interface to facilitate its use.

evolutionary biology↗

bioRxiv2019

Mechanical Feedback and Robustness of Apical Constrictions in Drosophila Embryo Ventral Furrow Formation

Formation of the ventral furrow in the Drosophila embryo relies on the apical constriction of cells in the ventral region to produce bending forces that drive tissue invagination. Recently [J Phys Condens Matter. 2016;28(41):414021], we observed that apical constrictions during the initial phase of ventral furrow formation produce elongated patterns of cellular constriction chains prior to invagination, and argued that these are indicative of tensile stress feedback. Here, we quantitatively analyze the constriction patterns preceding ventral furrow formation and find that they are consistent with the predictions of our active-granular-fluid model of a monolayer of mechanically coupled stress-sensitive constricting particles. Our model shows that tensile feedback causes constriction chains to develop along underlying precursor tensile stress chains that gradually strengthen with subsequent cellular constrictions. As seen in both our model and available optogenetic experiments, this mechanism allows constriction chains to penetrate or circumvent zones of reduced cell contractility, thus increasing the robustness of ventral furrow formation to spatial variation of cell contractility by rescuing cellular constrictions in the disrupted regions.

biophysics↗

bioRxiv2019

Hydraulic resistance of perivascular spaces in the brain

Perivascular spaces (PVSs) are annular channels that surround arteries and carry cerebrospinal fluid into the brain, sweeping away metabolic waste. In vivo observations reveal that they are not concentric, circular annuli, however: the outer boundaries are often oblate, and the arteries that form the inner boundaries are often offset from the central axis. Here we show that the observed shapes of PVSs have lower hydraulic resistance than concentric, circular annuli of the same size, and therefore allow faster, more efficient flow of cerebrospinal fluid. To calculate hydraulic resistance, we parameterize PVS cross-sections as circles surrounded by ellipses, varying the radii of the circles, major and minor axes of the ellipses, and two-dimensional eccentricities of the circles with respect to the ellipses. For each shape, we solve the governing Navier-Stokes equation to determine the velocity profile for steady laminar flow and the corresponding hydraulic resistance. We find that the minimum hydraulic resistance (and therefore maximum flow rate) for a given PVS cross-sectional area occurs when the ellipse is elongated and intersects the circle, dividing the PVS into two lobes, as is common around pial arteries. We also find that if both the inner and outer boundaries are circular, the minimum hydraulic resistance occurs when the eccentricity is large, as is common around penetrating arteries. The circular, concentric annuli assumed in recent studies maximize hydraulic resistance and therefore minimize flow. Our parameterization can incorporate more realistic resistances into hydraulic network models of flow of cerebrospinal fluid in the brain.\n\nSignificance StatementRecent experiments show that there is bulk flow of cerebrospinal fluid in brain perivascular spaces (PVSs) in the direction of the blood flow, driven by pulsations of arterial walls due to the heartbeat. Published hydraulic network models have argued against such a flow due to the purported high hydraulic resistance of the system. Here we show that these high resistances are due to misrepresentations of the size and shape of PVSs. We present an adjustable model PVS that can match closely the actual shapes observed in vivo and show that these shapes are often nearly optimal, in the sense of offering the least hydraulic resistance. This optimization may well represent an evolutionary adaptation that maximizes clearance of metabolic waste from the brain.

neuroscience↗

bioRxiv2017

Aquaporin-4 dependent glymphatic solute transport in rodent brain

The glymphatic system is a brain-wide metabolite clearance pathway, impairment of which in post-traumatic and ischemic brain or healthy aging is proposed to contribute to intracerebral accumulation of amyloid-{beta} and tau proteins. Glymphatic perivascular influx of cerebrospinal fluid (CSF) depends upon the expression and perivascular localization of the astroglial water channel aquaporin-4 (AQP4). Prompted by a recent publication that failed to find an effect of Aqp4 knockout on perivascular CSF tracer influx and interstitial fluid (ISF) tracer dispersion, four independent research groups have herein re-examined the importance of Aqp4 in glymphatic fluid transport. We concur in finding that CSF tracer influx, as well as fluorescently-tagged amyloid-{beta} efflux, are significantly faster in wild-type mice than in three different transgenic lines featuring disruption of the Aqp4 gene and one line in which AQP4 expression lacks the critical perivascular localization (Snta1 knockout). These data validate the role of AQP4 in supporting fluid and solute transport and efflux in brain in accordance with the glymphatic system model.

neuroscience↗

bioRxiv2017

Identification of a novel interspecific hybrid yeast from a metagenomic open fermentation sample using Hi-C

Interspecific hybridization is a common mechanism enabling genetic diversification and adaptation; however, the detection of hybrid species has been quite difficult. The identification of microbial hybrids is made even more complicated, as most environmental microbes are resistant to culturing and must be studied in their native mixed communities. We have previously adapted the chromosome conformation capture method Hi-C to the assembly of genomes from mixed populations. Here, we show the methods application in assembling genomes directly from an uncultured, mixed population from a spontaneously inoculated beer sample. Our assembly method has enabled us to de-convolute 4 bacterial and 4 yeast genomes from this sample, including a putative yeast hybrid. Downstream isolation and analysis of this hybrid confirmed its genome to consist of Pichia membranifaciens and that of another related, but undescribed yeast. Our work shows that Hi-C-based metagenomic methods can overcome the limitation of traditional sequencing methods in studying complex mixtures of genomes.

genomics↗