Biology subjects

Park, H.

Publications and source records attributed to Park, H..

At least 181 records · Page 10Linked to original sources

bioRxiv2020

Fast and easy single-molecule pulldown assay based on agarose microbeads

The recently developed single-molecule pulldown (SiMPull) assay by Jain and colleagues is a highly innovative technique but its wide application is hindered by the high technical barrier and time consumption. We report an innovative, agarose microbead-based approach for SiMPull. We used commercially available, pre-surface-functionalized agarose microbeads to capture the protein of interest together with its binding partners specifically from cell extracts and observed these interactions under a microscope at the single-molecule level. Relative to the original method, microbead-based SiMPull is considerably faster, easier to use, and more reproducible and yet provides similar sensitivity and signal-to-noise ratio; specifically, with the new method, sample-preparation time is substantially decreased (from [~]10 to [~]3 h). These crucial features should facilitate wide application of powerful and versatile SiMPull in common biological and clinical laboratories. Notably, by exploiting the simplicity and ultrahigh sensitivity of microbead-based SiMPull, we used this method in the study of rare auditory hair cells for the first time.

biochemistry↗

bioRxiv2020

Learning a force field from small-molecule crystal lattice predictions enables consistent sub-Angstrom protein-ligand docking

Accurate and rapid calculation of protein-small molecule interaction energies is critical for computational drug discovery. Because of the large chemical space spanned by drug-like molecules, classical force fields contain thousands of parameters describing atom-pair distance and torsional preferences; each parameter is typically optimized independently on simple representative molecules. Here we describe a new approach in which small-molecule force field parameters are jointly optimized guided by the rich source of information contained within thousands of available small molecule crystal structures. We optimize parameters by requiring that the experimentally determined molecular lattice arrangements have lower energy than all alternative lattice arrangements. Thousands of independent crystal lattice-prediction simulations were run on each of 1,386 small molecule crystal structures, and energy function parameters of an implicit solvent energy model were optimized so native crystal lattice arrangements had lowest energy. The resulting energy model was implemented in Rosetta, together with a rapid genetic algorithm docking method employing grid based scoring and receptor flexibility. The success rate of bound structure recapitulation in cross-docking on 1,112 complexes was improved by more than 10% over previously published methods, with solutions within <1 [A] in over half of the cases. Our results demonstrate that small molecule crystal structures are a rich source of information for systematically improving computational drug discovery.

biophysics↗

bioRxiv2020

Robust spatial ventriloquism effect and aftereffect under memory interference

Our brain adapts to discrepancies in the sensory inputs. One example is provided by the ventriloquism effect, experienced when the sight and sound of an object are displaced. Here the discrepant multisensory stimuli not only result in a biased localization of the sound, but also recalibrate the perception of subsequent unisensory acoustic information in the so-called ventriloquism aftereffect. This aftereffect has been linked to memory-related processes based on its parallels to general sequential effects in perceptual decision making experiments and insights obtained in neuroimaging studies. For example, we have recently implied memory-related medial parietal regions in the trial-by-trial ventriloquism aftereffect. Here, we tested the hypothesis that the ventriloquism aftereffect is indeed susceptible to manipulations interfering with working memory. Across three experiments we systematically manipulated the temporal delays between stimuli and response for either the ventriloquism or the aftereffect trials, or added a sensory-motor masking trial in between. Our data reveal no significant impact of either of these manipulations on the aftereffect, suggesting that the recalibration reflected by the ventriloquism aftereffect is surprisingly resilient to manipulations interfering with memory-related processes.

neuroscience↗

bioRxiv2020

Plant NLR targets P-type ATPase for executing plasma membrane depolarization leading to calcium influx and cell death

Hypersensitive response (HR) is a robust immune response mediated by plant nucleotide-binding and leucine-rich repeat receptor (NLR). However, the early molecular event linking NLR to cell death is obscure. Here we demonstrate that NLR targets plasma membrane H+-ATPases (PMA) generating electrochemical potential across the membrane. CCA309, an autoactive N-terminal domain of pepper coiled-coil NLR (CNL), associates with PMAs and its autoactivity is affected by silencing or overexpression of PMA. CCA309-induced extracellular alkalization accompanied with membrane depolarization is followed by calcium influx and cell death. CCA309 interacts with C-terminal regulatory domain of PMA and 14-3-3 negatively affects CCA309-induced cell death. Moreover, pharmacological experiments with fusicoccin, an irreversible PMA activator, confirmed that CC- and CNL-mediated cell death occurred through inhibiting PMA. We propose PMAs as the primary target of plasma membrane-associated CNL to disrupt electrochemical homeostasis leading to HR cell death.

plant biology↗

bioRxiv2020

Modular metabolite assembly in C. elegans lysosome-related organelles

Signaling molecules derived from attachment of diverse metabolic building blocks to ascarosides play a central role in the life history of C. elegans and other nematodes; however, many aspects of their biogenesis remain unclear. Using comparative metabolomics, we show that a pathway mediating formation of intestinal lysosome-related organelles (LROs) is required for biosynthesis of most modular ascarosides as well as previously undescribed modular glucosides. Similar to modular ascarosides, the modular glucosides are derived from highly selective assembly of moieties from nucleoside, amino acid, neurotransmitter, and lipid metabolism, suggesting that modular glucosides, like the ascarosides, may serve signaling functions. We further show that carboxylesterases that localize to intestinal organelles are required for the assembly of both modular ascarosides and glucosides via ester and amide linkages. Further exploration of LRO function and carboxylesterase homologs in C. elegans and other animals may reveal additional new compound families and signaling paradigms. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=158 SRC="FIGDIR/small/262956v2_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@6e83cborg.highwire.dtl.DTLVardef@18e9302org.highwire.dtl.DTLVardef@1557670org.highwire.dtl.DTLVardef@1d2ca50_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2020

Body mass variations relate to fractionated functional brain hierarchies

AO_SCPLOWBSTRACTC_SCPLOWVariations in body mass index (BMI) have been suggested to relate to atypical brain organization, yet connectome-level substrates of BMI and their neurobiological underpinnings remain unclear. Studying 325 healthy young adults, we examined association between functional connectome organization and BMI variations. We capitalized on connectome manifold learning techniques, which represent macroscale functional connectivity patterns along continuous hierarchical axes that dissociate low level and higher order brain systems. We observed an increased differentiation between unimodal and heteromodal association networks in individuals with higher BMI, indicative of an increasingly segregated modular architecture and a disruption in the hierarchical integration of different brain system. Transcriptomic decoding and subsequent gene enrichment analyses identified genes previously implicated in genome-wide associations to BMI and specific cortical, striatal, and cerebellar cell types. These findings provide novel insights for functional connectome substrates of BMI variations in healthy young adults and point to potential molecular associations.

neuroscience↗

bioRxiv2020

Constitutive androstane receptor directs T cell adaptation to bile acids in the small intestine

Bile acids (BAs) are lipid emulsifying metabolites synthesized in hepatocytes and maintained in vivo through enterohepatic circulation between the liver and small intestine1. As detergents, BAs can cause toxicity and inflammation in enterohepatic tissues2. Nuclear receptors maintain BA homeostasis in hepatocytes and enterocytes3, but it is unclear how mucosal immune cells tolerate high BA concentrations in the small intestine lamina propria (siLP). We previously reported that CD4+ T effector (Teff) cells upregulate expression of the xenobiotic transporter MDR1/ABCB1 in the siLP to prevent BA toxicity and suppress Crohns disease-like small bowel inflammation4. Here, we identify the nuclear xenobiotic receptor, constitutive androstane receptor (CAR/NR1I3), as a regulator of MDR1 expression in T cells, and safeguard against BA toxicity and inflammation in the small intestine. CAR was activated and induced large-scale transcriptional reprograming in Teff cells infiltrating the siLP, but not the colon. CAR induced expression of detoxifying enzymes and transporters in siLP Teff cells, as in hepatocytes, but also the key anti-inflammatory cytokine, Il10. Accordingly, CAR-deficiency in T cells exacerbated, whereas pharmacologic CAR activation suppressed, BA-driven ileitis in T cell-reconstituted Rag-/- mice. These data suggest that CAR acts locally in small intestinal T cells to detoxify BAs and resolve inflammation. Activation of this program offers an unexpected strategy to treat small bowel Crohns disease, and provides evidence of lymphocyte sub-specialization within the small intestine.

immunology↗

bioRxiv2020

A Versatile Soluble Siglec Scaffold for Sensitive and Quantitative Detection of Glycan Ligands

Sialic acid-binding immunoglobulin-type lectins (Siglecs) are immunomodulatory receptors that are regulated by their glycan ligands. A growing connection between Siglecs and human disease motivates improved methods to detect Siglec ligands. Here, we describe a new versatile set of Siglec-Fc proteins for glycan ligand detection. Enhanced sensitivity and selectivity are enabled through multimerization and avoiding Fc receptors, respectively. Using these Siglec-Fc proteins, Siglec ligands were systemically profiled on healthy and cancerous cells and tissues, revealing many unique patterns. Additional features enable the production of small, homogenous Siglec fragments and development of a quantitative ligand-binding mass spectrometry assay. Using this assay, the ligand specificities of several Siglecs were clarified. For CD33, we demonstrate that it recognizes both 2-3 and 2-6 sialosides in solution and on cells, which has implications for its link to Alzheimers disease susceptibility. These soluble Siglecs reveal the abundance of their glycan ligands on host cells as self-associated molecular patterns.

biochemistry↗

bioRxiv2020

Pyronaridine and artesunate are potential antiviral drugs against COVID-19 and influenza

Since the first human case was reported in Wuhan Province, China in December 2019, SARS-CoV-2 has caused millions of human infections in more than 200 countries worldwide with an approximately 4.01% case-fatality rate (as of 27 July, 2020; based on a WHO situation report), and COVID-19 pandemic has paralyzed our global community. Even though a few candidate drugs, such as remdesivir (a broad antiviral prodrug) and hydroxychloroquine, have been investigated in human clinical trials, their therapeutic efficacy needs to be clarified further to be used to treat COVID-19 patients. Here we show that pyronaridine and artesunate, which are the chemical components of anti-malarial drug Pyramax(R), exhibit antiviral activity against SARS-CoV-2 and influenza viruses. In human lung epithelial (Calu-3) cells, pyronaridine and artesunate were highly effective against SARS-CoV-2 while hydroxychloroquine did not show any effect at concentrations of less than 100 M. In viral growth kinetics, both pyronaridine and artesunate inhibited the growth of SARS-CoV-2 and seasonal influenza A virus in Calu-3 cells. Taken together, we suggest that artesunate and pyronaridine might be effective drug candidates for use in human patients with COVID-19 and/or influenza, which may co-circulate during this coming winter season.

microbiology↗

bioRxiv2020

Improved protein structure refinement guided by deep learning based accuracy estimation

We develop a deep learning framework (DeepAccNet) that estimates per-residue accuracy and residue-residue distance signed error in protein models and uses these predictions to guide Rosetta protein structure refinement. The network uses 3D convolutions to evaluate local atomic environments followed by 2D convolutions to provide their global contexts and outperforms other methods that similarly predict the accuracy of protein structure models. Overall accuracy predictions for X-ray and cryoEM structures in the PDB correlate with their resolution, and the network should be broadly useful for assessing the accuracy of both predicted structure models and experimentally determined structures and identifying specific regions likely to be in error. Incorporation of the accuracy predictions at multiple stages in the Rosetta refinement protocol considerably increased the accuracy of the resulting protein structure models, illustrating how deep learning can improve search for global energy minima of biomolecules.

bioinformatics↗

bioRxiv2020

Auditory detection is modulated by theta phase of silent lip movements

Audiovisual speech perception relies, among other things, on our expertise to map a speakers lip movements with speech sounds. This multimodal matching is facilitated by salient syllable features that align lip movements and acoustic envelope signals in the 4 - 8 Hz theta band. Although non-exclusive, the predominance of theta rhythms in speech processing has been firmly established by studies showing that neural oscillations track the acoustic envelope in the primary auditory cortex. Equivalently, theta oscillations in the visual cortex entrain to lip movements, and the auditory cortex is recruited during silent speech perception. These findings suggest that neuronal theta oscillations may play a functional role in organising information flow across visual and auditory sensory areas. We presented silent speech movies while participants performed a pure tone detection task to test whether entrainment to lip movements directs the auditory system and drives behavioural outcomes. We showed that auditory detection varied depending on the ongoing theta phase conveyed by lip movements in the movies. In a complementary experiment presenting the same movies while recording participants electro-encephalogram (EEG), we found that silent lip movements entrained neural oscillations in the visual and auditory cortices with the visual phase leading the auditory phase. These results support the idea that the visual cortex entrained by lip movements filtered the sensitivity of the auditory cortex via theta phase synchronisation.

neuroscience↗

bioRxiv2020

The neurophysiological basis of short- and long-term ventriloquism aftereffects

Our senses often receive conflicting multisensory information, which our brain reconciles by adaptive recalibration. A classic example is the ventriloquist aftereffect, which emerges following both long-term and trial-wise exposure to spatially discrepant multisensory stimuli. Still, it remains debated whether the behavioral biases observed following short- and long-term exposure arise from largely the same or rather distinct neural origins, and hence reflect the same or distinct mechanisms. We address this question by probing EEG recordings for physiological processes predictive of the single-trial ventriloquism biases following the exposure to spatially offset audio-visual stimuli. Our results support the hypothesis that both short- and long-term aftereffects are mediated by common neurophysiological correlates, which likely arise from sensory and parietal regions involved in multisensory inference and memory, while prolonged exposure to consistent discrepancies additionally recruits prefrontal regions. These results posit a central role of parietal regions in mediating multisensory spatial recalibration and suggest that frontal regions contribute to increasing the behavioral bias when the perceived sensory discrepancy is consistent and persistent over time.

neuroscience↗

bioRxiv2020

CCM 1 determines YAP/TAZ signaling dependent metastatic hallmarks of prostate cancer cells

Enhanced Yes-associated protein (YAP)/transcriptional co-activator with PDZ-binding motif (TAZ) signaling is correlated with the extraprostatic extension of prostate cancer. However, the mechanism by which YAP/TAZ signaling becomes hyperactive and drives prostate cancer progression is currently unclear. In this study, we demonstrated that CCM1 induces the metastasis of multiple types of prostate cancer cells by regulating YAP/TAZ signaling. Mechanistically, CCM1, a gene mutated in cerebral cavernous malformation, suppresses DDX5, which regulates the PLK1-mediated suppression of YAP/TAZ signaling, indicating that CCM1 and DDX5 are novel upstream regulators of YAP/TAZ signaling. We also revealed that higher expression of CCM1, which is uniquely found in advanced prostate cancer, is inversely correlated with metastasis-free and overall survival in patients with prostate cancer. Our findings highlight the importance of CCM1-DDX5-PLK1-YAP/TAZ signaling in the metastasis of prostate cancer cells. Statement of SignificanceOur analysis of CCM1 expression and function represents a candidate predictive biomarker for prostate cancer metastasis and provides an evidence that abnormality of CCM1 can be pathogenic in prostate cancer. Importantly, CCM1 regulation of metastasis progression appears to a common molecular event in metastatic prostate cancer cells arising in disparate genetic backgrounds.

cancer biology↗

bioRxiv2020

Prediction of protein mutational free energy: benchmark and sampling improvements increase classification accuracy

Software to predict the change in protein stability upon point mutation is a valuable tool for a number of biotechnological and scientific problems. To facilitate the development of such software and provide easy access to the available experimental data, the ProTherm database was created. Biases in the methods and types of information collected has led to disparity in the types of mutations for which experimental data is available. For example, mutations to alanine are hugely overrepresented whereas those involving charged residues, especially from one charged residue to another, are underrepresented. ProTherm subsets created as benchmark sets that do not account for this often underrepresented certain mutational types. This issue introduces systematic biases into previously published protocols ability to accurately predict the change in folding energy on these classes of mutations. To resolve this issue, we have generated a new benchmark set with these problems corrected. We have then used the benchmark set to test a number of improvements to the point mutation energetics tools in the Rosetta software suite.

bioengineering↗

bioRxiv2020

Diversification of perceptual mechanisms underlying preserved multisensory behaviour in healthy aging

The manner in which humans exploit multisensory information for subsequent decisions changes with age. Multiple causes for such age-effects are being discussed, including a reduced precision in peripheral sensory representations, changes in cognitive inference about causal relations between sensory cues, and a decline in memory contributing to altered sequential patterns of multisensory behaviour. To dissociate these putative contributions, we investigated how healthy young and older adults integrate audio-visual spatial information within trials (the ventriloquism effect) and between trials (the ventriloquism aftereffect). With both a model-free and (Bayesian) model-based analyses we found that both biases differed between groups. Our results attribute the age-change in the ventriloquism bias to a decline in spatial hearing rather than a change in cognitive processes. This decline in peripheral function, combined with a more prominent influence from preceding responses rather than preceding stimuli in the elderly, can also explain the observed age-effect in the ventriloquism aftereffect. Our results suggest a transition from a sensory- to a behavior-driven influence of past multisensory experience on perceptual decisions with age, due to reduced sensory precision and change in memory capacity.

neuroscience↗

bioRxiv2020

PICH translocase activity is required for proper distribution of SUMOylated proteins on mitotic chromosomes

Proper chromosome segregation is essential for faithful cell division and if not maintained results in defective cell function caused by abnormal distribution of genetic information. Polo-like kinase 1 interacting checkpoint helicase (PICH) is a DNA translocase essential in chromosome bridge resolution during mitosis. Its function in resolving chromosome bridges requires both DNA translocase activity and ability to bind chromosomal proteins modified by Small Ubiquitin-like modifier (SUMO). However, it is unclear how these activities are cooperating to resolve chromosome bridges. Here, we show that PICH specifically promotes the organization of SUMOylated proteins like SUMOylated TopoisomeraseIIα (TopoIIα) on mitotic chromosomes. Conditional depletion of PICH using the Auxin Inducible Degron (AID) system resulted in the retention of SUMOylated chromosomal proteins, including TopoIIα, indicating that PICH functions to control proper association of these proteins with chromosomes. Replacement of PICH with its mutants showed that PICH is required for the proper organization of SUMOylated proteins on chromosomes. In vitro assays showed that PICH specifically attenuates SUMOylated TopoIIα activity using its SUMO-binding ability. Taken together, we propose a novel function of PICH in remodeling SUMOylated proteins to ensure faithful chromosome segregation.Summary Statement Polo-like kinase interacting checkpoint helicase (PICH) interacts with SUMOylated proteins to mediate proper chromosome segregation during mitosis. The results demonstrate that PICH controls association of SUMOylated chromosomal proteins, including Topoisomerase IIα, and that function requires PICH translocase activity and SUMO binding ability.Competing Interest StatementThe authors have declared no competing interest.AbbreviationsTopoIIαTopoisomerase IIαPICHPolo-like kinase interacting checkpoint helicaseSPRStrand passage reactionSUMOSmall ubiquitin-like modifierXEEXenopus egg extractCSFCytostatic factordnUbc9dominant negative E2 SUMO-conjugating enzymeSENPSentrin-specific proteasePIASProtein inhibitor of activated STATSIMSUMO-interacting-motifView Full Text

cell biology↗

bioRxiv2019

Increased variability but intact integration during visual navigation in Autism Spectrum Disorder

Autism Spectrum Disorder (ASD) is a common neurodevelopmental disturbance afflicting a variety of functions from perception to cognition. The recent computational focus suggesting aberrant Bayesian inference in ASD has yielded promising but conflicting results in attempting to explain a wide variety of phenotypes by canonical computations. Here we used a naturalistic visual path integration task that combines continuous action with active sensing and allows tracking of subjects dynamic belief states. Both groups showed a previously documented bias pattern, by overshooting the radial distance and angular eccentricity of targets. For both control and ASD groups, these errors were driven by misestimated velocity signals due to a non-uniform speed prior, rather than imperfect integration. We tracked participants beliefs and found no difference in the speed prior, but heightened variability in the ASD group. Both end-point variance and trajectory irregularities correlated with ASD symptom severity. With feedback, variance was reduced and ASD performance approached that of controls. These findings highlight the need for both more naturalistic tasks and a broader computational perspective to understand the ASD phenotype and pathology.

neuroscience↗

bioRxiv2019

Design of DNA Origami Diamond Photonic Crystals

Self-assembled photonic crystals have proven to be a fascinating class of photonic materials for non-absorbing structural colorizations over large areas and in diverse relevant applications, including tools for on-chip spectrometers and biosensors, platforms for reflective displays, and templates for energy devices. The most prevalent building blocks for the self-assembly of photonic crystals are spherical colloids and block copolymers (BCPs) due to the generic appeal of these materials, which can be crafted into large-area 3D lattices. However, due to the intrinsic limitations of these structures, these two building blocks are difficult to assemble into a direct rod-connected diamond lattice, which is considered to be a champion photonic crystal. Here, we present a DNA origami-route for a direct rod-connected diamond photonic crystal exhibiting a complete photonic bandgap (PBG) in the visible regime. Using a combination of electromagnetic, phononic, and mechanical numerical analyses, we identify (i) the structural constraints of the 50 megadalton-scale giant DNA origami building blocks that could self-assemble into a direct rod-connected diamond lattice with high accuracy, and (ii) the elastic moduli that are essentials for maintaining lattice integrity in a buffer solution. A solution molding process could enable the transformation of the as-assembled DNA origami lattice into a porous silicon- or germanium-coated composite crystal with enhanced refractive index contrast, in that a champion relative bandwidth for the photonic bandgap (i.e., 0.29) could become possible even for a relatively low volume fraction (i.e., 16 vol%).

synthetic biology↗