Biology subjects

Park, K. Y.

Publications and source records attributed to Park, K. Y..

11 recordsLinked to original sources

bioRxiv2026

Drought Dominates Engineered Lipid Sink Effects on Sorghum Physiology and Carbon Allocation

Determining the environmental limits that govern how engineered metabolic traits control whole-plant carbon (C) allocation is essential for developing climate-resilient bioenergy systems. Oil-enhanced sorghum offers a promising strategy to boost aboveground energy density, yet its system-wide effects on root C investment and soil C delivery, particularly under drought, are largely uncharacterized. Here, we provide the first comprehensive assessment of these interactions using whole-plant 13CO2 continuous labeling, depth-specific sampling of roots and rhizosphere soil, and coordinated measurements of photosynthesis, stomatal anatomy, tissue nitrogen, and root non-structural carbohydrates (NSCs). Under well-watered conditions, oil enhancement produced distinct aboveground physiological changes, including slightly longer stomata, lower stomatal density, significantly higher leaf nitrogen concentration and biomass, and greater leaf 13C enrichment. Importantly, these aboveground changes did not translate into detectable shifts in the allocation of recent photosynthate to belowground pools. In contrast, drought acted as a dominant regulatory factor, reorganizing C flow across both genotypes by suppressing photosynthesis and leaf water status, increasing root nitrogen and NSC reserves, and significantly promoting the retention of recent assimilates in shallow root systems. Depth-specific 13C patterns showed that drought reduced new C incorporation into deep roots while increasing 13C enrichment in deep rhizosphere soil, suggesting that drought altered the balance between C investment in root growth and rhizodeposit C inputs at depth. Ultimately, soil moisture availability was an overriding determinant of belowground C partitioning and vertical C delivery, superseding the influence of the engineered lipid sink. These findings provide new mechanistic insight into the environmental constraints on C flow in an engineered bioenergy crop and identify moisture-driven limitations as the primary bottleneck for translating synthetic metabolic innovations into robust, ecosystem-level C outcomes.

ecology↗

bioRxiv2024

Aging and the Spectral Properties of Brain Hemodynamics

Cerebral glucose metabolism (CMRGlc) systematically decreases with advancing age. We sought to identify correlates of decreased CMRGlc in the spectral properties of fMRI signals imaged in the task-free state. We analyzed lifespan resting-state fMRI data acquired in 455 healthy adults (ages 18-87 years) and cerebral metabolic data acquired in a separate cohort of 94 healthy adults (ages 25-45 years, 65-85 years). We characterized the spectral properties of the fMRI data in terms of the relative predominance of slow vs. fast activity using the spectral slope (SS) measure. We found that the relative proportion of fast activity increases with advancing age (SS flattening) across most cortical regions. The regional distribution of spectral slope was topographically correlated with CMRGlc in young adults. Notably, whereas most older adults maintained a youthful pattern of SS topography, a distinct subset of older adults significantly diverged from the youthful pattern. This subset of older adults also diverged from the youthful pattern of CMRGlc metabolism. This divergent pattern was associated with T2-weighted signal changes in frontal lobe white matter, an independent marker of small vessel disease. These findings suggest that BOLD signal spectral slope flattening may represent a biomarker of age-associated neurometabolic pathology. Significance StatementAging is associated with a decline in cerebral glucose metabolism (CMRGlc). Here, we identified correlates of CMRGlc in the spectral properties of resting-state fMRI data using spectral slope (SS), which quantifies the relative predominance of slow vs. fast activity. We found that SS flattening with advancing age is most prominent in regions characterized by high CMRGlc in youth. A subset of older adults who diverged from the youthful pattern of SS topography also exhibited evidence of frontal lobe white matter pathology. These findings suggest that the spectral properties of rs-fMRI data provide mechanistic insights into age-related neuropathology. In particular, spectral slope measures may serve as early indicators of age-related neurometabolic decline and potentially identify individuals in whom intervention is indicated.

neuroscience↗

bioRxiv2024

Vibrotactile auricular vagus nerve stimulation alters limbic system connectivity in humans: A pilot study

Vibration offers a potential alternative modality for transcutaneous auricular vagus nerve stimulation (taVNS). However, mechanisms of action are not well-defined. The goal of this study was to evaluate the potential of vibrotactile stimulation as a method for activating central brain regions akin to other vagal nerve stimulation methodologies. To do so, intracranial electrophysiological signals were recorded in human subjects to perform a parametric characterization of vibrotactile taVNS and investigate changes in coherence across key brain regions. We hypothesized that vibrotactile taVNS would increase coherence between limbic brain areas, similar to areas activated by classic electrical VNS approaches. Our specific regions of interest included the orbitofrontal cortex, anterior cingulate cortex, amygdala, hippocampus, and parahippocampal gyrus. Patients with intractable epilepsy undergoing stereotactic electroencephalography (sEEG) monitoring participated in the study. Vibrotactile taVNS was administered across five vibration frequencies following a randomized stimulation on/off pattern, and sEEG signals were recorded throughout. Spectral coherence in response to stimulation was defined across four canonical frequency bands, theta, alpha, beta, and broadband gamma. At the group level, vibrotactile taVNS resulted in significantly increased global low-frequency coherence. Anatomically, multiple limbic brain regions exhibited notably increased coherence during taVNS compared to baseline. The percentage of total electrode pairs demonstrating increased coherence was also quantified at the individual level. 20 Hz vibration resulted in the highest percentage of responder pairs across low-frequency coherence measures, but notable inter-subject variability was present. Overall, vibrotactile taVNS induced significant low-frequency coherence increases involving several limbic system structures. Further, parametric characterization revealed the presence of inter-subject variability in terms of identifying the optimal vibration frequency. These findings encourage continued research into vibrotactile stimulation as an alternative modality for noninvasive vagus nerve stimulation.

neuroscience↗

bioRxiv2024

Enhancing lipid production in plant cells through high-throughput genome editing and phenotyping via a scalable automated pipeline

Plant bioengineering is a time-consuming and labor-intensive process, with no guarantee of achieving the desired trait. Here we report a fast, automated, scalable, high-throughput pipeline for plant bioengineering (FAST-PB). FAST-PB achieves gene cloning, genome editing, and product characterization by integrating automated biofoundry engineering of callus and protoplast cells with single cell matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). We first demonstrate that FAST-PB can streamline the Golden Gate cloning process, with the capacity to construct 96 vectors in parallel. To prove the concept, using FAST-PB, we first found that PEG2050 significantly increases transfection efficiency by over 45%. To validate the pipeline, we established a reporter-gene-free method for CRISPR editing via mutation of HCF136, affecting cellular chlorophyll fluorescence. Next, we applied this pipeline for lipid production and found that diverse lipids were significantly enhanced up to sixfold through introducing multi-gene cassettes via CRISPR activation, and regenerated plant using this platform. Lastly, we harnessed FAST-PB to achieve high-throughput single-cell lipid profiling through the integration of MALDI-MS with the biofoundry, and differentiated engineered and unengineered cells using the single-cell lipidomics. These innovations massively increase the throughput of synthetic biology, genome editing, and metabolic engineering, and change what is possibly using single-cell metabolomics in plants.

synthetic biology↗

bioRxiv2022

Innate immune cell response to host-parasite interaction in a human intestinal tissue microphysiological system

Protozoan parasites that infect humans are widespread, and lead to varied clinical manifestations, including life-threatening illnesses in immunocompromised individuals. Animal models have provided insight into innate immunity against parasitic infections, however, species-specific differences and complexity of innate immune responses make translation to humans challenging. Thus, there is a need for novel in vitro systems that can elucidate mechanisms of immune control and parasite dissemination. We have developed a human microphysiological system of intestinal tissue to evaluate parasite-immune-specific interactions during infection, which integrates primary intestinal epithelial cells and immune cells to investigate the role of innate immune cells during epithelial infection by the protozoan parasite, Toxoplasma gondii, which affects billions of people worldwide. Our data indicate that epithelial-infection by parasites stimulates a broad range of effector functions in neutrophils and NK cell-mediated cytokine production that play immunomodulatory roles, demonstrating the potential of our system for advancing the study of human-parasite interactions. TeaserNovel engineered model of human intestinal tissue for study of dissemination and immune control of parasitic infections.

bioengineering↗

bioRxiv2021

Leukocyte proliferation mediates disease pathogenesis in the Ndufs4(KO) mouse model of Leigh syndrome

Symmetric, progressive, necrotizing lesions in the brainstem are a defining feature of Leigh syndrome (LS). A mechanistic understanding of the pathogenesis of these lesions has been elusive. Here, we report that leukocyte proliferation is causally involved in the pathogenesis of Leigh syndrome. Directly depleting leukocytes with a colony-stimulating factor 1 receptor (CSF1R) inhibitor dramatically attenuates disease, including complete prevention of CNS lesion formation and substantial extension of survival. Leukocyte depletion rescues a range of symptoms including hyperlactemia, seizures, respiratory function, and neurologic symptoms. These data provide a mechanistic explanation for the beneficial effects of mTOR inhibition. More importantly, these findings dramatically alter our understanding of the pathogenesis of LS, demonstrating that immune involvement directly drives disease. These findings have significant implication for the mechanisms of disease resulting from mitochondrial dysfunction, and may lead to novel therapeutic strategies. One-Sentence SummaryPharmacologic targeting of leukocytes prevents CNS lesions, neurological disease, and metabolic dysfunction in the Ndufs4(KO) mouse model of Leigh syndrome.

pathology↗

bioRxiv2021

Translocation of chloroplast NPR1 to the nucleus in retrograde signaling for adaptive response to salt stress in tobacco

Chloroplasts play a pivotal role in biotic and abiotic stress responses, accompanying changes in the cell reduction/oxidation (redox) state. Chloroplasts are an endosymbiotic organelle that sends retrograde signals to the nucleus to integrate with environmental changes. This study showed that salt stress causes the rapid accumulation of the nonexpressor of pathogenesis-related genes 1 (NPR1) protein, a redox-sensitive transcription coactivator that elicits many tolerance responses in chloroplasts and the nucleus. The transiently accumulated chloroplast NPR1 protein was translocated to the nucleus in a redox-dependent manner under salinity stress. In addition, immunoblotting and fluorescence image analysis showed that chloroplast-targeted NPR1-GFP fused with cTP (chloroplast transit peptide from RbcS) was localized in the nucleus during the responses to salt stress. Chloroplast functionality was essential for retrograde translocation, in which the stomules and cytoplasmic vesicles participated. Treatments with H2O2 and an ethylene precursor enhanced this retrograde translocation. Compared to each wild-type plant, retrograde signaling-related gene expression was severely impaired in the npr1-1 mutant in Arabidopsis, but enhanced transiently in the NPR1-Ox transgenic tobacco line. Therefore, NPR1 might be a retrograde signaling hub that improves a plants adaptability to changing environments.

plant biology↗

bioRxiv2020

Under-oil autonomously regulated oxygen microenvironments for cell culture

Oxygen levels in vivo are autonomously regulated by a supply-demand balance, which can be altered in disease states. However, the oxygen levels of in vitro cell culture systems, particularly microscale cell culture, are typically dominated by either supply or demand. Further, the oxygen microenvironment in these systems are rarely monitored or reported. Here, we present a method to establish and dynamically monitor autonomously regulated oxygen microenvironments (AROM) using an oil overlay in an open microscale cell culture system. Using this method, the oxygen microenvironment is dynamically regulated via a supply-demand balance of the system. We simulate the kinetics of oxygen diffusion in multiliquid-phase microsystems on COMSOL Multiphysics and experimentally validate the method using a variety of cell types including mammalian, fungal and bacterial cells. Finally, we demonstrate the utility of this method to establish a co-culture between primary intestinal epithelial cells and a highly prevalent human gut species Bacteroides uniformis.

bioengineering↗

bioRxiv2020

Mechanisms underlying neonate specific metabolic effects of volatile anesthetics

Volatile anesthetics (VAs) are widely used in medicine, but the mechanisms underlying their effects remain ill-defined. Though routine anesthesia is safe in healthy individuals, instances of sensitivity are well-documented, and there has been significant concern regarding the impact of VAs on neonatal brain development. Evidence indicates that VAs have multiple targets, with anesthetic and non-anesthetic effects mediated by neuroreceptors, ion channels, and the mitochondrial electron transport chain. Here, we characterize an unexpected metabolic effect of VAs in neonatal mice. Neonatal blood {beta}-hydroxybutarate ({beta}-HB) is rapidly depleted by VAs at concentrations well below those necessary for anesthesia. {beta}-HB in adults, including animals in dietary ketosis, is unaffected. Depletion of {beta}-HB is mediated by citrate accumulation, malonyl-CoA production by acetyl-CoA carboxylase, and inhibition of fatty acid oxidation. Adults show similar significant changes to citrate and malonyl-CoA, but are insensitive to malonyl-CoA, displaying reduced metabolic flexibility compared to younger animals.

physiology↗

bioRxiv2020

Phytosphingosine induces systemic acquired resistance through activation of sphingosine kinase

Phytosphingosine (PHS) is a naturally occurring bioactive sphingolipid molecule. Intermediates such as sphingolipid long-chain bases (LCBs) in sphingolipid biosynthesis have been shown to have important roles as signaling molecules. In this study, exogenous addition of PHS caused rapid induction of transcripts responsible for transient synthesis of LCBs, reactive oxygen species, and ethylene. These events were followed by the induction of sphingolipid kinase (SphK), which metabolized PHS to phytosphingosine-1-phosphate in an biphasic manner. PHS alleviated not only pathogen-induced cell damage but also reduced the growth of virulent pathogens in the entire upper part of the PHS-treated plant stem during the necrotic stage after inoculation, suggesting the development of systemic acquired resistance (SAR) and plant immunity. Moreover, PHS treatment up-regulated the transcription and activity of SphK, accompanied by prominent increases in the transcription levels of serine palmitoyltransferase (LCB1 and LCB2) for de novo synthesis of sphingolipids, as well as ROS-detoxifying enzymes and PR proteins at 48 h after virulent pathogen infection. The impairment of ROS production at this time is more beneficial for the activation of SphK and inhibition of pathogenicity during the necrotic stage of hemibiotrophic infection, indicating that necrotic cell death at the late stage is regulated by ROS-independent SphK. Phosphorylated LCBs significantly reduced pathogen-induced cell damage. These observations suggest that selective channeling of sphingolipids into phosphorylated forms in a time-dependent manner has a pro-survival effect by promoting SAR in plant immunity. 4. One Sentence SummarySelective gene expression in sphingolipid biosynthesis and channeling into their phosphorylated forms are significant determinants of their roles as pro-survival signaling molecules.

plant biology↗

bioRxiv2019

The Molecular Basis for Nestmate Recognition in the Eusocial Ant Camponotus floridanus

BackgroundIn eusocial ants, aggressive behaviors require a sophisticated ability to detect and discriminate between chemical signatures such as cuticular hydrocarbons that distinguish nestmate friends from non-nestmate foes. It has been suggested that a mismatch between a chemical signature (label) and the internal, neuronal representation of the colony odor (template) leads to the recognition of and subsequent aggression between non-nestmates. While several studies have demonstrated that ant chemosensory systems, most notably olfaction, are largely responsible for the decoding of these chemical signatures, a definitive demonstration that odorant receptors are responsible for the detection and processing of the pheromonal signals that regulate nestmate recognition has thus far been lacking. To address this, we have developed an aggression-based bioassay incorporating a suite of highly selective odorant receptor modulators to characterize the role of olfaction in nestmate recognition in the formicine ant Camponotus floridanus.\n\nResultsValidation of our aggression-based behavioral assay was carried out by demonstrating an antennal requirement for nestmate recognition. In order to adapt this bioassay for the volatile delivery of Orco modulators, electroantennography was used to show that both a volatilized Orco antagonist (VUANT1) and an Orco agonist (VUAA4) eliminated or otherwise interfered with the electrophysiological responses to the hydrocarbon decane, respectively. Volatilize administration of these compounds to adult workers significantly reduced aggression between non-nestmates without altering aggression levels between nestmates but did not alter aggressive responses towards a mechanical stimulus.\n\nConclusionsOur studies provide direct evidence that the antennae (as olfactory appendages) and odorant receptors (at the molecular level) are necessary for mediating aggression towards non-nestmates. Furthermore, our observations support a hypothesis in which rejection of non-nestmates depends on the precise detection and decoding of chemical signatures present on non-nestmates as opposed to the absence of any information or the active acceptance of familiar signatures. In addition to describing a novel approach to assess olfactory signaling in genetically intractable insect systems, these studies contribute to a long-standing interest in odor coding and the molecular neuroethology of nestmate recognition.

ecology↗