Biology subjects

Casey, C.

Publications and source records attributed to Casey, C..

12 recordsLinked to original sources

bioRxiv2025

The cytochrome P450 enzyme MpCYP78E1 inhibits meristem initiation and activity in Marchantia polymorpha

Plant shoot branches are formed by the initiation and activation of generative centres known as meristems. In dichotomously branching plants, such as many bryophytes and lycophytes, new meristems are formed when a pre-existing meristem splits into two daughter meristems. These meristems may be active and produce shoot branches or may be inactive. Here, we show that in conditions where meristem inactivation occurs, such as simulated shade, the position of the inactive meristem alternated between either side of the plant body in the liverwort Marchantia polymorpha. Using this predictable pattern, we generated transcriptomes of active and inactive meristems and identified the cytochrome P450 monooxygenase, MpCYP78E1, as a novel regulator of meristem activity. MpCYP78E1 reporter expression was higher in active meristems than inactive meristems. More meristems were active in loss of function mutants than wild type, and fewer meristems were active in gain of function mutants, indicating that MpCYP78E1 inhibits meristem activity. Furthermore, unlike wild type, Mpcyp78e1 loss of function mutants produced supernumerary meristem from the centre of the mature plant body. We conclude that MpCYP78E1 inhibits both meristem initiation and activity to modulate shoot branching architecture.

plant biology↗

bioRxiv2025

Wing Hinge Dynamics Influence Stroke Amplitudes in Flapping Wing Insects: A Frequency Response Approach

Flapping wing insects leverage the dynamics of their compliant flight systems to reduce the energetic costs of flying. However, the extent to which the wing hinge dynamics contribute to the overall system dynamics remains unknown. Therefore, we developed an approach to (1) quantify the passive dynamic properties of the wing hinge, and (2) identify the resonant frequency of the isolated wing/wing hinge system. First, we measured the frequency response relating thorax deformation to wing stroke angle in sacrificed honeybees and army cutworm moths. Using these data, we developed a linear model of the flight system, which we then extended to incorporate nonlinear effects associated with large wing stroke angles. Our findings revealed that both species flap below the linear resonance of the wing hinge. At larger angles, nonlinear aerodynamic damping reduces the resonant frequency, causing both species to flap above wing hinge resonance. We discuss how wing-thorax coupling and muscle dynamics may cause the resonant frequency of the entire flight system to deviate from that of the wing/wing hinge system. Our estimates of wing hinge stiffness and damping provide quantitative parameters that can be incorporated into models of the insect flight system to enable more accurate predictions of resonance behavior.

biophysics↗

bioRxiv2024

Turgor pressure affects transverse stiffness and resonant frequencies of buzz-pollinated poricidal anther

Several agriculturally valuable plants store their pollen in tube-like poricidal anthers, which release pollen through buzz pollination. In this process, bees rapidly vibrate the anther using their indirect flight muscles. The stiffness and resonant frequency of the anther are crucial for effective pollen release, yet the impact of turgor pressure on these properties is not well understood. Here, we perform three-point flexure tests and experimental modal analysis to determine anther transverse stiffness and resonant frequency, respectively. Dynamic nanoindentation is used to identify the anthers storage modulus as a function of excitation frequency. We subsequently develop mathematical models to estimate how turgor pressure changes after the anther is removed from a flower, thereby emulating zero water availability. We find that 30 minutes post-ablation, anther stiffness decreases 60%. Anther resonant frequency decreases 20% 60 minutes post-ablation. Models indicate turgor pressure in the fresh anther is about 0.2 - 0.3 MPa. Our findings suggest that natural fluctuations in turgor pressure due to environmental factors like temperature and light intensity may require bees to adjust their foraging behaviors. Interestingly, anther storage modulus increased with excitation frequency, underscoring the need for more sophisticated mechanical models that consider viscous fluid transport through plant tissue moving forward.

biophysics↗

bioRxiv2024

Birds affected by a 2021 avian mortality event are strongly associated with supplemental feeding and ground foraging behaviors

In 2021, news outlets and state natural resources agencies reported a large number of avian deaths across several states in the eastern and midwestern USA. This event fomented a rapid and robust response from animal health experts from across the country. Given the clustered pattern of disease and death, an infectious etiology was rigorously investigated. No single causative pathogen was identified, leaving the cause and thus epidemiology of the mortality event unex-plained. In this study, we attempted to hone in on potential causes or contributors to this event by constructing a dataset on affected birds life history, phylogeny, and ecology. After a preliminary analysis of these features, we developed a statistical pipeline to test two hypotheses regarding features of birds associated with the mortality event: (1) that a significant proportion of affected birds in the total sample are members of the Cornell Feederwatch list (i.e., birds that consume supplemental feed, and their predators), and that (2) ground-feeding species would be significantly represented in the sample. While logistic regression models support the plausibility of the two hypotheses, they are statistically indistinguishable. We discuss the implications of these findings, propose future work, and highlight the importance of ecological and behavioral expertise in understanding epidemiological phenomena.

ecology↗

bioRxiv2023

Translating electrophysiological signatures of awareness into thalamocortical mechanisms by inverting systems-level computational models across arousal states

While consciousness never fades during wakefulness, there is a paradoxical coexistence of consciousness during dreaming states. Its also possible for sensory awareness to be either present or absent when awakened from seemingly-identical states of sedation and anaesthesia. Traditionally, these states have been characterised in terms of their electroencephalographic neural correlates, however, without clear underlying neurobiological mechanisms. To bridge this gap, we invert a validated neural mass model of the corticothalamic system using scalp EEG collected during nonlinear transitions in conscious experience and sensory awareness across varying depths of dexmedetomidine sedation. We found that a decline in conscious experience and sensory awareness with dexmedetomidine was associated with a decrease in the engagement of excitatory thalamocortical loop resonances, along with an increase in inhibitory intrathalamic loop gains. These findings shed light into the neural mechanisms of conscious experience and sensory awareness, and explain how it fades across arousal states, bridging the gap between the neural correlates of consciousness and its underlying systems-level thalamocortical mechanisms.

neuroscience↗

bioRxiv2023

Efficient differential expression analysis of large-scale single cell transcriptomics data using dreamlet

Advances in single-cell and -nucleus transcriptomics have enabled generation of increasingly large-scale datasets from hundreds of subjects and millions of cells. These studies promise to give unprecedented insight into the cell type specific biology of human disease. Yet performing differential expression analyses across subjects remains difficult due to challenges in statistical modeling of these complex studies and scaling analyses to large datasets. Our open-source R package dreamlet (DiseaseNeurogenomics.github.io/dreamlet) uses a pseudobulk approach based on precision-weighted linear mixed models to identify genes differentially expressed with traits across subjects for each cell cluster. Designed for data from large cohorts, dreamlet is substantially faster and uses less memory than existing workflows, while supporting complex statistical models and controlling the false positive rate. We demonstrate computational and statistical performance on published datasets, and a novel dataset of 1.4M single nuclei from postmortem brains of 150 Alzheimers disease cases and 149 controls.

genomics↗

bioRxiv2022

Reduced coenzyme Q synthesis confers non-target site resistance to the herbicide thaxtomin A

Herbicide resistance in weeds is a growing threat to global crop production. Non-target site resistance is problematic because a single resistance allele can confer tolerance to many herbicides (cross resistance), and it is often a polygenic trait so it can be difficult to identify the molecular mechanisms involved. Most characterized molecular mechanisms of non-target site resistance are caused by gain-of-function mutations in genes from a few key gene families - the mechanisms of resistance caused by loss-of-function mutations remain unclear. In this study, we first show that the mechanism of non-target site resistance to the herbicide thaxtomin A conferred by loss-of-function of the gene PAM16 is conserved in Marchantia polymorpha, validating its use as a model species with which to study non-target site resistance. To identify mechanisms of non-target site resistance caused by loss-of-function mutations, we generated 107 UV-B mutagenized M. polymorpha spores and screened for resistance to the herbicide thaxtomin A. We isolated 13 thaxtomin A-resistant mutants and found that 3 mutants carried candidate resistance-conferring SNPs in the MpRTN4IP1L gene. Mprtn4ip1l mutants are defective in coenzyme Q biosynthesis and accumulate higher levels of reactive oxygen species (ROS) than wild-type plants. Mutants are also defective in thaxtomin A metabolism, consistent with the hypothesis that loss of MpRTN4IP1L function confers non-target site resistance. We conclude that loss of MpRTN4IP1L function is a novel mechanism of non-target site herbicide resistance, and propose that other mutations which increase ROS levels or decrease thaxtomin A metabolism could confer thaxtomin A resistance in the field. AUTHOR SUMMARYModern agriculture relies on herbicides to control weed populations. However, herbicide resistance in weeds threatens the efficacy of herbicides and global crop production, similar to how antibiotic resistance poses a global health threat. Understanding the molecular mechanisms behind herbicide resistance helps to prevent resistance from evolving and to better manage herbicide resistant weeds in the field. Here, we use a forward genetic approach in the model species Marchantia polymorpha to discover novel mechanisms of herbicide resistance. We report the discovery of a novel mechanism of herbicide resistance caused by loss-of-function mutations in the MpRTN4IP1L gene. We find that Mprtn4ip1l mutants are resistant to the herbicides thaxtomin A and isoxaben, accumulate higher levels of reactive oxygen species than wild type plants, and are defective in thaxtomin A metabolism. We predict that loss-of-function mutations or treatments that increase reactive oxygen species production could contribute to thaxtomin A tolerance.

plant biology↗

bioRxiv2021

Experimental Studies of Carpenter Bee (Xylocopa: Apidae) Thorax Mechanics During Defensive Buzzing

Approximately 10% of flowering plant species conceal their pollen within tube-like poricidal anthers. Bees extract pollen from poricidal anthers via floral buzzing, a behavior during which they apply cyclic forces by biting the anther and rapidly contracting their flight muscles. The success of pollen extraction during floral buzzing relies on the direction and magnitude of the forces applied by the bees, yet these forces and forcing directions have not been previously quantified. In this work, we developed an experiment to simultaneously measure the directional forces and thorax kinematics produced by carpenter bees (Xylocopa californica) during defensive buzzing, a behavior regulated by similar physiological mechanisms as floral buzzing. We found that the buzzing frequencies averaged about 130 Hz and were highly variable within individuals. Force amplitudes were on average 170 mN, but at times reached nearly 500 mN. These forces were 30 - 80 times greater than the weight of the bees tested. The two largest forces occurred within a plane formed by the bees flight muscles. Force amplitudes were moderately correlated with thorax displacement, velocity and acceleration amplitudes but only weakly correlated with buzzing frequency. Linear models developed through this work provide a mechanism to estimate forces produced during non-flight behaviors based on thorax kinematic measurements in carpenter bees. Based on the buzzing frequencies, individual bees capacity to vary buzz frequency and predominant forcing directions, we hypothesize that carpenter bees leverage vibration amplification to increase the deformation of poricidal anthers, and hence the amount of pollen ejected.

biophysics↗

bioRxiv2021

The flying insect thoracic cuticle is heterogenous in structure and in thickness-dependent modulus gradation

The thorax is a specialized structure central to an insects ability to fly. In the thorax, flight muscles are surrounded by a thin layer of cuticle. The structure, composition, and material properties of this chitinous structure may influence the efficiency of the thorax in flight. However, these properties, as well as their variation throughout anatomical regions of the thorax or between insect taxa, are not known. In this work, we provide a multi-faceted assessment of thorax cuticle for fliers with asynchronous (honey bee; Apis mellifera) and synchronous (hawkmoth; Manduca sexta) muscles. We investigated cuticle structure using histology, material composition through confocal laser scanning microscopy, and modulus gradation with nanoindentation. Our results suggest that cuticle properties of the thorax are highly dependent on anatomical region and species. Modulus gradation, but not mean modulus, differed between the two types of fliers. In some regions, A. mellifera had a positive linear modulus gradient from cuticle interior to exterior of about 2 GPa. In M. sexta, the modulus gradients were variable and were not well represented by linear fits with respect to cuticle thickness. We utilized finite element modeling to assess how measured modulus gradients influenced maximum stress in cuticle. Stress was reduced when cuticle with a linear gradient was compressed from the high modulus side. These results support the protective role of the A. mellifera thorax cuticle. Our multi-faceted assessment advances our understanding of thorax cuticle structural and material heterogeneity and the potential benefit of material gradation to flying insects. Graphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY Statement of SignificanceThe insect thorax is essential for efficient flight but questions remain about the contribution of exoskeletal cuticle. We assessed the thorax cuticle using a high resolution multi-faceted approach to determine how cuticle properties vary within thorax anatomical regions and between fliers with asynchronous (honey bee; Apis mellifera) and synchronous (hawkmoth; Manduca sexta) muscles. We examined structure using histological staining, modulus using nanoindentation, and material composition using confocal scanning light microscopy. We further utilized finite element modeling to understand the effect of the modulus gradations observed experimentally on stress accumulation. Cuticle properties vary through cuticle thickness, by thorax region, and between flight lineages.

biophysics↗

bioRxiv2020

Matrix Stiffness Regulates Liver Sinusoidal Endothelial Cell Function Mimicking Responses in Fatty Liver Disease

Liver sinusoidal endothelial cells (LSECs) are a highly specialized endothelial cell that participates in numerous liver metabolic activities and collectively function as a scavenger system in the liver by removing waste macromolecules playing a vital role in the balance of lipids, cholesterol, and vitamins. Prior to hepatic fibrosis, independent of their etiology, LSECs become highly pro-inflammatory, capillarized (loss in fenestrations), and loss in specialized receptors (Stabilin-1, Stabilin-2, CD31 and SE-1). Liver fibrosis also leads to significant loss in the endocytosis function of LSECs. Thus understanding regulation of LSEC phenotype may be critical to understanding fibrosis. Extensive remodeling of the extracellular matrix occurs during fibrosis that leads to liver stiffening. The role of matrix stiffness as related to subtle but pivotal changes in LSECs physiology is under explored. The overall goal of our study is the development and implementation of a platform that enables the convergence of engineered cell microenvironments with the phenotypic and functional analysis of LSECs. Using our innovative biomimetic liver fibrosis model that allows modulation of substrate stiffness, we investigated the role of liver matrix stiffness in modulating LSECs function in fibrotic-like microenvironment. Primary LSECs were cultured on our novel polymer film coated polydimethylsiloxane (PDMS) gels with 2 kPa, 9 kPa 25 kPa and 55 kPa elastic modulus mimicking healthy, early fibrotic, fibrotic and extremely fibrotic substrates. SEM was used to image to fenestrations of LSECs and HA endocytosis assay was performed to measure the LSECs function. LSECs cultured on stiffer environment had significant remodeling of cytoskeletal proteins and morphology indicated of stress fibers. Also we observed that LSECs on fibrotic substrates resulted in loss of fenestrations (capillarization). This is critical as capillarization has been show to precede hepatic fibrosis and "capillarized" LSECs lose the ability to promote hepatic stellate cell (HSC) quiescence. LSECs on stiffer environment also had higher expression of cell adhesion molecules, VCAM-1 and ICAM-1 indicating the loss of phenotype of the cells. Fibrotic stiffness also impeded the HA endocytosis in LSECs, one of the main functions of the cells. These data suggest a plausible mechanism that increased stiffness modulates hepatocyte and LSEC function causing liver functional failure. Similar effect was observed in LSECs isolated from Non-Alcoholic Fatty Liver Disease (NAFLD) rat models indicating correlation to physiological conditions. Together, all these data demonstrates the plausible role of stiffness in regulating LSECs function and contribute to HSC activation and progression of liver fibrosis.

bioengineering↗

bioRxiv2020

Receptors, circuits and neural dynamics for prediction

Learned associations between stimuli allow us to model the world and make predictions, crucial for efficient behavior; e.g., hearing a siren, we expect to see an ambulance and quickly make way. While there are theoretical and computational frameworks for prediction, the circuit and receptor-level mechanisms are unclear. Using high-density EEG, Bayesian modeling and machine learning, we show that inferred "causal" relationships between stimuli and frontal alpha activity account for reaction times (a proxy for predictions) on a trial-by-trial basis in an audio-visual delayed match-to-sample task which elicited predictions. Predictive beta feedback activated sensory representations in advance of predicted stimuli. Low-dose ketamine, a NMDA receptor blocker - but not the control drug dexmedetomidine - perturbed behavioral indices of predictions, their representation in higher-order cortex, feedback to posterior cortex and pre-activation of sensory templates in higher-order sensory cortex. This study suggests predictions depend on alpha activity in higher-order cortex, beta feedback and NMDA receptors, and ketamine blocks access to learned predictive information.

neuroscience↗

bioRxiv2018

Golgi Renaissance: the pivotal role of the largest Golgi protein giantin

Golgi undergoes disorganization in response to the drugs or alcohol, but it is able to restore compact structure under recovery. This self-organization mechanism remains mostly elusive, as does the role of giantin, the largest Golgi matrix dimeric protein. Here, we found that in cells treated with Brefeldin A (BFA) or ethanol (EtOH), Golgi disassembly is associated with giantin de-dimerization, which was restored to the dimer form after BFA or EtOH washout. Cells lacking giantin are disabled for the restoration of the classical ribbon Golgi, and they demonstrate altered trafficking of proteins to the cell surface. The fusion of the nascent Golgi membranes is mediated by the cross-membrane interaction of Rab6a GTPase and giantin. Giantin is involved in the formation of long intercisternal connections, which in giantin-depleted cells was replaced by the short bridges that formed via oligomerization of GRASP65. This phenomenon occurs in advanced prostate cancer cells, in which a fragmented Golgi phenotype is maintained by the dimerization of GRASP65. Thus, we provide a model of Golgi Renaissance, which is impaired in aggressive prostate cancer.

cell biology↗