Biology subjects

Han, S.

Publications and source records attributed to Han, S..

At least 235 records · Page 13Linked to original sources

bioRxiv2020

Chloroquine and hydroxychloroquine as ACE2 blockers to inhibit viropexis of COVID-19 Spike psedotype virus

BackgroundThe novel coronavirus disease (2019-nCoV) has been affecting global health since the end of 2019 and there is no sign that the epidemic is abating. The major issue for controlling the infectious is lacking efficient prevention and therapeutic approaches. Chloroquine (CQ) and Hydroxychloroquine (HCQ) have been reported to treat the disease, but the underlying mechanism remains controversial. PurposeThe objective of this study is to investigate whether CQ and HCQ could be ACE2 blockers and used to inhibit 2019-nCoV virus infection. MethodsIn our study, we used CCK-8 staining, flow cytometry and immunofluorescent staining to evaluate the toxicity and autophagy of CQ and HCQ, respectively, on ACE2 high-expressing HEK293T cells (ACE2h cells). We further analyzed the binding character of CQ and HCQ to ACE2 by molecular docking and surface plasmon resonance (SPR) assays, 2019-nCoV spike pseudotyped virus was also used to observe the viropexis effect of CQ and HCQ in ACE2h cells. ResultsResults showed that HCQ is slightly more toxic to ACE2h cells than CQ. Both CQ and HCQ could bind to ACE2 with KD =(7.31{+/-}0.62)e-7 M and (4.82{+/-}0.87)e-7 M, respectively. They exhibit equivalent suppression effect for the entrance of 2019-nCoV spike pseudotyped virus into ACE2h cells. ConclusionsCQ and HCQ both inhibit the entrance 2019-nCoV into cells by blocking the binding of the virus with ACE2. Our findings provide novel insights into the molecular mechanism of CQ and HCQ treatment effect on virus infection.

biochemistry↗

bioRxiv2020

The Proline-rich Domain Promotes Tau Liquid Liquid Phase Separation in Cells

Tau protein in vitro can undergo liquid liquid phase separation (LLPS); however, observations of this phase transition in living cells are limited. To investigate protein state transitions in living cells we found that Cry2 can optogentically increase the association of full lengh tau with microtubules. To probe this mechanism, we identified tau domains that drive tau clustering on microtubules in living cells. The polyproline rich domain (PRD) drives LLPS and does so under the control of phosphorylation. These readily observable cytoplasmic condensates underwent fusion and fluorescence recovery after photobleaching consistent with the ability of the PRD to undergo LLPS in vitro. In absence of the MTBD, the tau PRD co-condensed with EB1, a regulator of plus-end microtubule dynamic instability. The specific domain properties of the MTBD and PRD serve distinct but mutually complementary roles that utilize LLPS in a cellular context to implement emergent functionalities that scale their relationship from binding alpha-beta tubulin heterodimers to the larger proportions of microtubules.

neuroscience↗

bioRxiv2020

SIRT1 ameliorates premature senescence-induced defenestration in hepatic sinusoidal endothelial cell

Premature senescence, linked to progerin, involves in endothelial dysfunction and liver diseases. Activating sirtuin 1 (SIRT1) ameliorates liver fibrosis. However, the potential mechanisms of premature senescence in defenestration in hepatic sinusoidal endothelial cells (HSECs) and how SIRT1 affects fenestrae remains elusive. Our study showed that in vivo, premature senescence occurred, with decrease of SIRT1, during CCl4-induced defenestration in HSECs and liver fibrogenesis; whereas overexpressing SIRT1 with adenovirus vector lessened progerin-associated premature senescence to relieve CCl4-induced defenestration and liver fibrosis. In vitro, fenestrae in HSECs disappeared, with progerin-associated premature senescence; these effects aggravated by H2O2-induced oxidative damage. Nevertheless, knockdown of NOX2 or overexpression of SIRT1 with adenovirus vector reduced progerin-associated premature senescence to maintain fenestrae through deacetylating p53. Furthermore, more Ac p53 K381 and progerin co-localized with accumulation of actin filament (F-actin) in the nuclear envelope of H2O2-treated HSECs; in contrast, these effects were rescued by overexpressing SIRT1. In conclusion, NOX2-dependent oxidative damage aggravates defenestration in HSECs via progerin-associated premature senescence; SIRT1-mediated deacetylation of p53 maintains fenestrae and attenuates liver fibrogenesis through inhibiting premature senescence.

cell biology↗

bioRxiv2020

Background white noise and speech facilitate visual working memory

In contrast to background white noise, the detrimental effects of background speech on verbal working memory (WM) were often explained by speech interference in the same verbal modality. Yet, those results were confounded with potential differences between arousal levels induced by speech and white noise. To address the role of arousal, in the present study, we minimized the verbal interference and used a visual WM task to test the influence of background speech or white noise. Electrodermal activity (EDA) and Electromyography (EMG) were recorded simultaneously to indicate the arousal levels of participants. Results showed that both background speech and white noise significantly improved visual WM performance. The change of performance further correlated with the change of physiological signals linked with arousal. Taken together, our results suggest that both background speech and white noise facilitate visual WM through raising the arousal level.

physiology↗

bioRxiv2020

Behavioral and neural decomposition of skull-induced death awareness

Death awareness influences multiple aspects of human lives, but its psychological constructs and underlying brain mechanisms remain unclear. We address these by measuring behavioral and brain responses to images of human skulls. We show that skulls relative to control stimuli delay responses to life-related words but speed responses to death-related words. Skulls compared to the control stimuli induce early deactivations in the posterior ventral temporal cortex followed by activations in the posterior and anterior ventral temporal cortices. The early and late neural modulations by perceived skulls respectively predict skull-induced changes of behavioral responses to life- and death-related words and the early neural modulation further predicts death anxiety. Our findings decompose skull-induced death awareness into two-stage neural processes of a lifeless state of a former life. One sentence summaryBehavioral and brain imaging findings decompose skull-induced death awareness into two-stage neural processes of a lifeless state of a former life.

neuroscience↗

bioRxiv2020

Lectin-like Intestinal Defensin Inhibits 2019-nCoV Spike binding to ACE2

The burgeoning epidemic caused by novel coronavirus 2019 (2019-nCoV) is currently a global concern. Angiotensin-converting enzyme-2 (ACE2) is a receptor of 2019-nCoV spike 1 protein (S1) and mediates viral entry into host cells. Despite the abundance of ACE2 in small intestine, few digestive symptoms are observed in patients infected by 2019-nCoV. Herein, we investigated the interactions between ACE2 and human defensins (HDs) specifically secreted by intestinal Paneth cells. The lectin-like HD5, rather than HD6, bound ACE2 with a high affinity of 39.3 nM and weakened the subsequent recruitment of 2019-nCoV S1. The cloak of HD5 on the ligand-binding domain of ACE2 was confirmed by molecular dynamic simulation. A remarkable dose-dependent preventive effect of HD5 on 2019-nCoV S1 binding to intestinal epithelial cells was further evidenced by in vitro experiments. Our findings unmasked the innate defense function of lectin-like intestinal defensin against 2019-nCoV, which may provide new insights into the prevention and treatment of 2019-nCoV infection.

microbiology↗

bioRxiv2020

ZmCLA4 regulates leaf angle through multiple plant hormone-mediated signal pathways in maize

Leaf angle in cereals is an important agronomic trait contributing to plant architecture and grain yield by determining the plant compactness. Although ZmCLA4 was identified to shape plant architecture by affecting leaf angle, the detailed regulatory mechanism of ZmCLA4 in maize remains unclear. ZmCLA4 was identified as a transcriptional repressor using the Gal4-LexA/UAS system and transactivation analysis in yeast. The DNA affinity purification (DAP)-seq assay showed that ZmCLA4 not only acts as a repressor containing the EAR motif (CACCGGAC), but was also found to have two new motifs, CCGARGS and CDTCNTC. On analyzing the ZmCLA4-bound targeted genes, we found that ZmCLA4, as a cross node of multiple plant hormone-mediated pathways, directly bound to ARF22 and IAA26 to regulate auxin transport and mediated brassinosteroid signaling by directly binding to BZR3 and 14-3-3. ZmCLA4 bound two WRKY genes involved with abscisic acid, two genes (CYP75B1, CYP93D1) involved with jasmonic acid, B3 involved in the response to ethylene, and thereby negatively regulated leaf angle formation. We built a new regulatory network for the ZmCLA4 gene controlling leaf angle in maize, which contributed to the understanding of ZmCLA4s regulatory mechanism and will improve grain yields by facilitating optimization of plant architecture.

molecular biology↗

bioRxiv2020

RNA-protein interaction mapping via MS2 or Cas13-based APEX targeting

RNA-protein interactions underlie a wide range of cellular processes. Improved methods are needed to systematically map RNA-protein interactions in living cells in an unbiased manner. Capitalizing on the ability of the engineered peroxidase APEX2 to identify protein interaction partners via proximity-dependent biotinylation, we used two approaches to target APEX2 to specific cellular RNAs. Both an MS2-MCP system and an engineered CRISPR-Cas13 system were able to deliver APEX2 to the human telomerase RNA hTR with high specificity. One-minute proximity biotinylation captured endogenous protein interaction partners of hTR, including more than a dozen proteins not previously linked to hTR. We validated the unexpected interaction between hTR and the N6-methyladenosine (m6A) demethylase ALKBH5. Further investigation showed that endogenous hTR is modified by m6A, which can be erased by ALKBH5, and that ALKBH5 influences both telomerase complex assembly and activity. These results highlight the ability of MS2- and Cas13-targeted APEX2 to identify novel RNA-protein interactions in living cells.

molecular biology↗

bioRxiv2020

Identification of a novel breathing circuit that controls pain and anxiety

Alleviating pain with controlled breathing has been practiced throughout human history. Despite its wide use and long history, a neural circuit-based understanding of the pain-breathing interaction is largely lacking. Here we report a novel breathing circuit that regulates non-homeostatic breathing rhythm, as well as pain and anxiety. We identify that a cluster of neurons expressing the Oprm1 gene, which encodes the -opioid receptor (MOR) in the lateral subdivision of parabrachial nucleus (PBLOprm1), directly regulates breathing rate in mice by conveying signals from the limbic areas to respiratory rhythm generating neurons in the medullary preBotzinger Complex (preBotC). In addition, we found that pain signals rapidly increase breathing rate by activating these neurons in both awake and anesthetized mice. Inactivating these neurons not only decreases the breathing rate, but it also substantially decreases anxiety-like behaviors and induces strong appetitive behaviors. Furthermore, PBLOprm1 inactivation alleviates pain by attenuating the perception of the affective-motivational aspect of pain. These results suggest that PBLOprm1 neurons play a critical role in the non-homeostatic regulation of breathing and in the regulation of pain and anxiety through breathing.

neuroscience↗

bioRxiv2019

Prolonged anesthesia alters brain synaptic architecture

Prolonged medically-induced coma (pMIC), a procedure performed in millions of patients worldwide, leads to cognitive impairment, yet the underlying brain mechanism remains unknown. No experimental studies of medically-induced coma (MIC) exceeding ~6 hours exist. For MIC of less than 6 hours, studies in developing rodents have documented transient changes of cortical synapse formation. However, in adulthood, cortical synapses are thought to become stabilized. Here, we establish pMIC (up to 24 hrs) in adolescent and mature mice, and combine repeated behavioral object recognition assessments with longitudinal two-photon imaging of cortical synapses. We find that pMIC affects cognitive function, and is associated with enhanced synaptic turnover, generated by enhanced synapse formation during pMIC, while the post-anesthetic period is dominated by synaptic loss. These results carry profound implications for intensive medical care, as they point out at significant structural side effects of pMIC on cortical brain synaptic architecture across age levels.

neuroscience↗

bioRxiv2019

Satellite cell depletion in early adulthood attenuates muscular dystrophy pathogenesis

Satellite cells are skeletal muscle resident stem cells that regenerate adult myofibers following an acute injury to muscle. Despite the assumption that the loss of satellite cells would be detrimental in a chronic regeneration-inducing muscle disease such as muscular dystrophy, this assumption has never been tested using mouse genetics. Here we generated a novel model of satellite cell ablation and crossed it with mouse models of muscular dystrophy to directly investigate how critical these cells are in maintaining muscle during a chronic degenerative disorder. Satellite cell deletion in 2-week-old young dystrophic mice provided noticeable improvements in histopathology and function, although at this early timepoint it was utimately detrimental because muscle size was not sufficient to permit survival. However, depletion of satellite cells beginning at 2 months of age in dystrophic mice provided similar histological and functional improvements but without compromising muscle size. The improved profile showed fewer damaged fibers, less myofiber central nucleation, increased sarcolemma integrity, decreased fibrosis and a dramatic size increase in the remaining myofibers. At the functional level, young adult dystrophic mice lacking satellite cells performed significantly better than those with satellite cells when exercised on a treadmill. Thus, loss of satellite cells during early adulthood in dystrophic mice produces an unexpected protective effect.

molecular biology↗

bioRxiv2019

Reorienting Spatial Attention within Visual Working Memory

Attention and working memory (WM) are intertwined core cognitive processes. Through four experiments with 133 participants, we dissociated the impact of two types of covert spatial attention, endogenous vs. exogenous, on visual WM. Behavioral results consistently indicated that exogenous attentional cues were more advantageous than endogenous ones in enhancing the precision of visual WM under load-2, while they equalized under load-4. In addition, physiological and neural data explained the mechanisms. Converging evidence from eye-tracking, electroencephalography, and magnetoencephalography suggested that fast attentional processing induced by exogenous cues lead to early top-down information from the dorsal lateral prefrontal cortex (DLPFC) to sensory cortices. The differential frontal activities were further correlated with the behavioral distinctions between exogenous and endogenous cues, and transcranial magnetic stimulation over DLPFC at the same time period abolished the exogenous advantage. Taken together, traditionally considered bottom-up attentional processing induced by exogenous cues rapidly engages top-down signals from the frontal cortex, which leads to stronger behavioral benefits compared with the benefits produced by endogenous cues under the low load condition.

neuroscience↗

bioRxiv2019

Rapid antimicrobial susceptibility test using spatiotemporal analysis of laser speckle dynamics of bacterial colonies

Antimicrobial susceptibility testing (AST) is crucial for providing appropriate choices and doses of antibiotics to patients. However, standard ASTs require a time-consuming incubation of about 16-20 h for visual accumulation of bacteria, limiting the use of AST for an early prescription. In this study, we propose a rapid AST based on laser speckle formation (LSF) that enables rapid detection of bacterial growth, with the same sample preparation protocol as in solid-based ASTs. The proposed method exploits the phenomenon that well-grown bacterial colonies serve as optical diffusers, which convert a plane-wave laser beam into speckles. The generation of speckle patterns indicates bacterial growth at given antibiotic concentrations. Speckle formation is evaluated by calculating the spatial autocorrelation of speckle images, and bacterial growth is determined by tracking the autocorrelation value over time. We demonstrated the performance of the proposed method for several combinations of bacterial species and antibiotics to achieve the AST in 2-4.5 hours. Furthermore, we also demonstrated the sensitivity of the technique for low bacterial density. The proposed method can be a powerful tool for rapid, simple, and low-cost AST. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=160 SRC="FIGDIR/small/853168v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@8ee314org.highwire.dtl.DTLVardef@de47c5org.highwire.dtl.DTLVardef@13a0103org.highwire.dtl.DTLVardef@118ad36_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2019

Neural correlates of episodic memory modulated by temporally delayed rewards

When a stimulus is associated with an external reward, its chance of being consolidated into long-term memory is boosted via dopaminergic facilitation of long-term potentiation in the hippocampus. Given that higher temporal distance (TD) has been found to discount the subjective value of a reward, we hypothesized that memory performance associated with a more immediate reward will result in better memory performance. We tested this hypothesis by measuring both behavioral memory performance and brain activation using functional magnetic resonance imaging (fMRI) during memory encoding and retrieval tasks. Contrary to our hypothesis, both behavioral and fMRI results suggest that the TD of rewards might enhance the chance of the associated stimulus being remembered. The fMRI data demonstrate that the lateral prefrontal cortex, which shows encoding-related activation proportional to the TD, is reactivated when searching for regions that show activation proportional to the TD during retrieval. This is not surprising given that this region is not only activated to discriminate between future vs. immediate rewards, it is also a part of the retrieval-success network. These results provide support for the conclusion that the encoding-retrieval overlap provoked as the rewards are more delayed lead to better memory performance of the items associated with the rewards.

neuroscience↗

bioRxiv2019

A Bayesian method for rare variant analysis using functional annotations and its application to Autism

Rare variant analysis is commonly used in whole-exome or genome sequencing studies. Compared to common variants, rare variants tend to have larger effect sizes and often directly point out causal genes. These potential benefits make association analysis with rare variants a priority for human genetics researchers. To improve the power of such studies, numerous methods have been developed to aggregate information of all variants of a gene. However, these gene-based methods often make unrealistic assumptions, e.g. the commonly used burden test effectively assumes that all variants chosen in the analysis have the same effects. In practice, current methods are often underpowered. We propose a Bayesian method: MIxture model based Rare variant Analysis on GEnes (MIRAGE). MIRAGE analyzes summary statistics, i.e. variant counts from inherited variants in trio-sequencing or from ancestry-matched case-control studies. MIRAGE captures the heterogeneity of variant effects by treating all variants of a gene as a mixture of risk and non-risk variants, and uses external information of variants to model the prior probabilities of being risk variants. We demonstrate in both simulations and analysis of an exome-sequencing dataset of autism, that MIRAGE significantly outperforms current methods for rare variant analysis. The top genes identified by MIRAGE are highly enriched with known or plausible autism risk genes. MIRAGE is available at https://xinhe-lab.github.io/mirage.

genetics↗

bioRxiv2019

Cell-Surface Proteomic Profiling in the Fly Brain Uncovers New Wiring Regulators

Molecular interactions at the cellular interface mediate organized assembly of single cells into tissues, and thus govern the development and physiology of multicellular organisms. Here, we developed a cell-type-specific, spatiotemporally-resolved approach to profile cell-surface proteomes in intact tissues. Quantitative profiling of cell-surface proteomes of Drosophila olfactory projection neurons (PNs) in pupae and adults revealed a global down-regulation of wiring molecules and an up-regulation of synaptic molecules in the transition from developing to mature PNs. A proteome-instructed in vivo screen identified 20 new cell-surface molecules regulating neural circuit assembly, many of which belong to evolutionarily conserved protein families not previously linked to neural development. Genetic analysis further revealed that the lipoprotein receptor LRP1 cell-autonomously controls PN dendrite targeting, contributing to the formation of a precise olfactory map. These findings highlight the power of temporally-resolved in situ cell-surface proteomic profiling in discovering new regulators of brain wiring.

neuroscience↗

bioRxiv2019

Three-dimensional label-free observation of individual bacteria upon antibiotic treatment using optical diffraction tomography

Measuring alterations in bacteria upon antibiotic application is important for basic studies in microbiology, drug discovery, and clinical diagnosis, and disease treatment. However, imaging and 3D time-lapse response analysis of individual bacteria upon antibiotic application remain largely unexplored mainly due to limitations in imaging techniques. Here, we present a method to systematically investigate the alterations in individual bacteria in 3D and quantitatively analyze the effects of antibiotics. Using optical diffraction tomography, in-situ responses of Escherichia coli and Bacillus subtilis to various concentrations of ampicillin were investigated in a label-free and quantitative manner. The presented method reconstructs the dynamic changes in the 3D refractive-index distributions of living bacteria in response to antibiotics at sub-micrometer spatial resolution.

microbiology↗

bioRxiv2019

Isometric exercise facilitates attention to salient events in women via the noradrenergic system

The locus coeruleus (LC) plays a critical role in regulating attention via the release of norepinephrine (NE), with levels of tonic LC activity constraining the intensity of phasic LC responses. However, the effects of manipulating tonic LC-NE activity on phasic activity have yet to be demonstrated in humans. In the current fMRI study, we used isometric handgrip to modulate tonic LC-NE activity in the time period immediately afterwards. During this post-handgrip time, an oddball detection task was used to probe how changes in tonic arousal influenced functional coordination between the LC and a right frontoparietal network that supports attentional selectivity. As expected, the frontoparietal network responded more to infrequent target and novel sounds than to frequent sounds. Across participants, greater LC-frontoparietal functional connectivity, pupil dilation, and faster oddball detection were all positively associated with LC MRI contrast from a neuromelanin-sensitive structural scan. Thus, LC structural integrity was related to LC functional dynamics and attentional performance during the oddball task. We also found that handgrip led to larger phasic pupil responses to oddball sounds, faster oddball detection speed, and greater frontoparietal network activation, suggesting that something that induces strong LC activity benefits attentional performance for at least the next few minutes. In addition, older women showed a similar benefit of handgrip on frontoparietal network activation as younger women, despite showing lower frontoparietal network activation overall. Together these findings suggest that a simple exercise may improve selective attention in healthy aging, at least for several minutes afterwards.\n\nHighlightsO_LIWe examined how handgrip affects arousal-attention dynamics during an oddball task\nC_LIO_LISalient stimuli enhanced pupil dilation and were detected faster post-handgrip\nC_LIO_LIA decrease in tonic pupil size after handgrip suggests norepinephrine depletion\nC_LIO_LIMRI-assessed LC integrity was related to oddball detection and pupil dilation\nC_LIO_LILC integrity also associated with LC-frontoparietal network functional connectivity\nC_LI

neuroscience↗