Biology subjects

Gu, C.

Publications and source records attributed to Gu, C..

69 records · Page 4Linked to original sources

bioRxiv2020

Potent antiviral effect of protoporphyrin IX and verteporfin on SARS-CoV-2 infection

The SARS-CoV-2 infection is spreading rapidly worldwide. Efficacious antiviral therapeutics against SARS-CoV-2 is urgently needed. Here, we discovered that protoporphyrin IX (PpIX) and verteporfin, two FDA-approved drugs, completely inhibited the cytopathic effect produced by SARS-CoV-2 infection at 1.25 M and 0.31 M respectively, and their EC50 values of reduction of viral RNA were at nanomolar concentrations. The selectivity indices of PpIX and verteporfin were 952.74 and 368.93, respectively, suggesting broad margin of safety. Importantly, PpIX and verteporfin prevented SARS-CoV-2 infection in mice adenovirally transduced with human ACE2. The compounds, sharing a porphyrin ring structure, were shown to bind viral receptor ACE2 and interfere with the interaction between ACE2 and the receptor-binding domain of viral S protein. Our study suggests that PpIX and verteporfin are potent antiviral agents against SARS-CoV-2 infection and sheds new light on developing novel chemoprophylaxis and chemotherapy against SARS-CoV-2.

microbiology↗

bioRxiv2020

Cortical ChAT+ neurons co-transmit acetylcholine and GABA in a target- and brain-region specific manner

The cerebral cortex contains neurons that express choline acetyltransferase (ChAT) and are a potential local source of acetylcholine. However, the neurotransmitters released by cortical ChAT+ neurons and their synaptic connectivity are unknown. We show that the nearly all cortical ChAT+ neurons are specialized VIP+ interneurons that release GABA strongly onto other inhibitory interneurons and acetylcholine sparsely onto layer 1 interneurons and other VIP+/ChAT+ interneurons. This differential transmission of ACh and GABA based on the postsynaptic target neuron is reflected in VIP+/ChAT+ interneuron pre-synaptic terminals, as quantitative molecular analysis shows that only a subset of these are specialized to release acetylcholine. In addition, we identify a separate, sparse population of non-VIP ChAT+ neurons in the medial prefrontal cortex with a distinct developmental origin that robustly release acetylcholine in layer 1. These results demonstrate both cortex-region heterogeneity in cortical ChAT+ interneurons and target-specific co-release of acetylcholine and GABA.

neuroscience↗

bioRxiv2020

Fully human single-domain antibodies against SARS-CoV-2

The COVID-19 pandemic is spreading rapidly, highlighting the urgent need for an efficient approach to rapidly develop therapeutics and prophylactics against SARS-CoV-2. We describe here the development of a phage-displayed single-domain antibody library by grafting naive CDRs into framework regions of an identified human germline IGHV allele. This enabled the isolation of high-affinity single-domain antibodies of fully human origin. The panning using SARS-CoV-2 RBD and S1 as antigens resulted in the identification of antibodies targeting five types of neutralizing or non-neutralizing epitopes on SARS-CoV-2 RBD. These fully human single-domain antibodies bound specifically to SARS-CoV-2 RBD with subnanomolar to low nanomolar affinities. Some of them were found to potently neutralize pseudotyped and live virus, and therefore may represent promising candidates for prophylaxis and therapy of COVID-19. This study also reports unique immunogenic profile of SARS-CoV-2 RBD compared to that of SARS-CoV and MERS-CoV, which may have important implications for the development of effective vaccines against SARS-CoV-2.

microbiology↗

bioRxiv2019

Nick-seq for single-nucleotide resolution genomic maps of DNA modifications and damage

Here we present the Nick-seq platform for quantitative mapping of DNA modifications and damage at single-nucleotide resolution across genomes. Pre-existing breaks are blocked and DNA structures converted to strand-breaks for 3-extension by nick-translation to produce nuclease-resistant oligonucleotides, and 3-capture by terminal transferase tailing. Libraries from both products are subjected to next-generation sequencing. Nick-seq is a generally applicable method illustrated with quantitative profiling of single-strand-breaks, phosphorothioate modifications, and DNA oxidation.

molecular biology↗

bioRxiv2019

From competing motor plans to a single action within a single trial on the human motor periphery

Contemporary motor control theories propose competition between multiple motor plans before the winning command is executed. While most competitions are completed prior to movement onset, movements are often initiated before the competition has been resolved. An example of this is saccadic averaging, wherein the eyes land at an intermediate location between two visual targets. Behavioral and neurophysiological signatures of competing motor commands have also been reported for reaching movements, but debate remains about whether such signatures attest to an unresolved competition, arise from averaging across many trials, or reflect a strategy to optimize behavior given task constraints. Here, we recorded electromyographic activity from an upper limb muscle (m. pectoralis) while twelve (8 female) participants performed an immediate response reach task, freely choosing between one of two identical and suddenly presented visual targets. On each trial, muscle recruitment showed two distinct phases of directionally-tuned activity. In the first wave, time-locked ~100 ms of target presentation, muscle activity was clearly influenced by the non-chosen target, reflecting a competition between reach commands that was biased in favor of the ultimately chosen target. This resulted in an initial movement intermediate between the two targets. In contrast, the second wave, time-locked to voluntary reach onset, was not biased toward the non-chosen target, showing that the competition between targets was resolved. Instead, this wave of activity compensated for the averaging induced by the first wave. Thus, single-trial analysis reveals an evolution in how the non-chosen target differentially influences the first and second wave of muscle activity. SIGNIFICANCE STATEMENTContemporary theories of motor control suggest that multiple motor plans compete for selection before the winning command is executed. Evidence for this is found in intermediate reach movements towards two potential target locations, but recent findings have challenged this notion by arguing that intermediate reaching movements reflect an optimal response strategy. By examining upper limb muscle recruitment during a free-choice reach task, we show early recruitment of a sub-optimal averaged motor command to the two targets that subsequently transitions to a single motor command that compensates for the initially averaged motor command. Recording limb muscle activity permits single-trial resolution of the dynamic influence of the non-chosen target through time.

neuroscience↗

bioRxiv2019

Stimulus-Locked Responses on Human Upper Limb Muscles and Corrective Reaches are Preferentially Evoked by Low Spatial Frequencies

In situations requiring immediate action, humans can generate visually-guided responses at remarkably short latencies. Here, to better understand the visual attributes that best evoke such rapid responses, we recorded upper limb muscle activity while participants performed visually-guided reaches towards Gabor patches composed of differing spatial frequencies. We studied reaches initiated from a stable posture (experiment 1, a static condition), or during on-line reach corrections to an abruptly displaced target (experiment 2, a dynamic condition). In both experiments, we detail the latency and prevalence of stimulus-locked responses (SLRs), which are brief bursts of EMG activity that are time-locked to target presentation rather than movement onset. SLRs represent the first wave of EMG recruitment influenced by target presentation, and enable quantification of rapid visuomotor transformations. In both experiments, reach targets composed of low spatial frequencies elicited the shortest latency and most prevalent SLRs, with SLR latency increasing and SLR prevalence decreasing for reach targets composed of progressively higher spatial frequencies. SLRs could be evoked in either the static or dynamic condition, and when present in experiment 2, were associated with shorter latency and larger magnitude corrections. Furthermore, SLRs evolved at shorter latencies (~20 ms) when the arm was already in motion. These results demonstrate that stimuli composed of low spatial frequencies preferentially evoke the most rapid visuomotor responses which, in the context of rapidly correcting an on-going reaching movement, are associated with earlier and larger on-line reach corrections.\n\nSignificance StatementHumans have a remarkable capacity to respond quickly to changes in our visual environment. Although our visual world is composed of a range of spatial frequencies, surprisingly little is known about which frequencies preferentially evoke rapid reaching responses. Here, we systematically varied the spatial frequency of peripheral reach targets while measuring EMG activity on an upper limb muscle. We found that visual stimuli composed of low-spatial frequencies elicit the most rapid and robust EMG responses and corrective reaches. Thus, when time is of the essence, low spatial frequencies preferentially drive fast visuomotor responses.

neuroscience↗

bioRxiv2019

Suppression of transcytosis regulates zebrafish blood-brain barrier development

As an optically transparent model organism with an endothelial blood-brain barrier (BBB), zebrafish offer a powerful tool to study the vertebrate BBB. However, the precise developmental profile of functional zebrafish BBB acquisition and the subcellular and molecular mechanisms governing the zebrafish BBB remain poorly characterized. Here we find a spatiotemporal gradient of barrier acquisition. Moreover, we capture the dynamics of developmental BBB leakage using live imaging, revealing a combination of steady accumulation in the parenchyma and sporadic bursts of tracer leakage. Electron microscopy studies further reveal that this steady accumulation results from high levels of transcytosis that are eventually suppressed, sealing the BBB. Finally, we demonstrate a key mammalian BBB regulator Mfsd2a, which inhibits transcytosis, plays a conserved role in zebrafish. Mfsd2aa mutants display increased larval and adult BBB permeability due to increased transcytosis. Our findings indicate a conserved developmental program of barrier acquisition between zebrafish and mice.

developmental biology↗

bioRxiv2018

Target-specific co-transmission of acetylcholine and GABA from a subset of cortical VIP+ interneurons

The modulation of cortex by acetylcholine (ACh) is typically thought to originate from long-range projections arising in the basal forebrain. However, a subset of VIP interneurons express ChAT, the synthetic enzyme for ACh, and are a potential local source of cortical ACh. Which neurotransmitters these VIP/ChAT interneurons (VCINs) release is unclear, and which post-synaptic cell types these transmitters target is not known. Using quantitative molecular analysis of VCIN pre-synaptic terminals, we show expression of the molecular machinery to release both ACh and GABA, with ACh release restricted to a subset of boutons. A systematic survey of potential post-synaptic cell types shows that VCINs release GABA primarily onto other inhibitory interneuron subtypes, while ACh neurotransmission is notably sparse, with most ACh release onto layer 1 interneurons and other VCINs. Therefore, VCINs are an alternative source of cortical ACh signaling that supplement GABA-mediated disinhibition with highly targeted excitation through ACh.

neuroscience↗

bioRxiv2018

Effect of a Sepsis Prediction Algorithm on Patient Mortality, Length of Stay, and Readmission

ObjectiveTo validate performance of a machine learning algorithm for severe sepsis determination up to 48 hours before onset, and to evaluate the effect of the algorithm on in-hospital mortality, hospital length of stay, and 30-day readmission.\n\nSettingThis cohort study includes a combined retrospective analysis and clinical outcomes evaluation: a dataset containing 510,497 patient encounters from 461 United States health centers for retrospective analysis, and a multiyear, multicenter clinical data set of real-world data containing 75,147 patient encounters from nine hospitals for clinical outcomes evaluation.\n\nParticipantsFor retrospective analysis, 270,438 adult patients with at least one documented measurement of five out of six vital sign measurements were included. For clinical outcomes analysis, 17,758 adult patients who met two or more Systemic Inflammatory Response Syndrome (SIRS) criteria at any point during their stay were included.\n\nResultsAt severe sepsis onset, the MLA demonstrated an AUROC of 0.91 (95% CI 0.90, 0.92), which exceeded those of MEWS (0.71, P<001), SOFA (0.74; P<.001), and SIRS (0.62; P<.001). For severe sepsis prediction 48 hours in advance of onset, the MLA achieved an AUROC of 0.77 (95% CI 0.73, 0.80). For the clinical outcomes study, when using the MLA, hospitals saw an average 39.5% reduction of in-hospital mortality, a 32.3% reduction in hospital length of stay, and a 22.7% reduction in 30-day readmission rate.\n\nConclusionsThe MLA accurately predicts severe sepsis onset up to 48 hours in advance using only readily available vital signs in retrospective validation. Reductions of in-hospital mortality, hospital length of stay, and 30-day readmissions were observed in real-world clinical use of the MLA. Results suggest this system may improve severe sepsis detection and patient outcomes over the use of rules-based sepsis detection systems.\n\nKEY POINTSO_ST_ABSQuestionC_ST_ABSIs a machine learning algorithm capable of accurate severe sepsis prediction, and does its clinical implementation improve patient mortality rates, hospital length of stay, and 30-day readmission rates?\n\nFindingsIn a retrospective analysis that included datasets containing a total of 585,644 patient encounters from 461 hospitals, the machine learning algorithm demonstrated an AUROC of 0.93 at time of severe sepsis onset, which exceeded those of MEWS (0.71), SOFA (0.74), and SIRS (0.62); and an AUROC of 0.77 for severe sepsis prediction 48 hours in advance of onset. In an analysis of real-world data from nine hospitals across 75,147 patient encounters, use of the machine learning algorithm was associated with a 39.5% reduction in in-hospital mortality, a 32.3% reduction in hospital length of stay, and a 22.7% reduction in 30-day readmission rate.\n\nMeaningThe accurate and predictive nature of this algorithm may encourage early recognition of patients trending toward severe sepsis, and therefore improve sepsis related outcomes.\n\nSTRENGTHS AND LIMITATIONS OF THIS STUDYO_LIA retrospective study of machine learning severe sepsis prediction from a dataset with 510,497 patient encounters demonstrates high accuracy up to 48 hours prior to onset.\nC_LIO_LIA multicenter clinical study of real-world data using this machine learning algorithm for severe sepsis alerts achieved reductions of in-hospital mortality, length of stay, and 30-day readmissions.\nC_LIO_LIThe required presence of an ICD-9 code to classify a patient as severely septic in our retrospective analysis potentially limits our ability to accurately classify all patients.\nC_LIO_LIOnly adults in US hospitals were included in this study.\nC_LIO_LIFor the real-world section of the study, we cannot eliminate the possibility that implementation of a sepsis algorithm raised general awareness of sepsis within a hospital, which may lead to higher recognition of septic patients, independent of algorithm performance.\nC_LI

bioinformatics↗

bioRxiv2018

A rapid visuomotor response on the human upper limb is selectively influenced by implicit, but not explicit, motor learning

How do humans learn to adapt their motor actions to achieve task success? Recent behavioral and patient studies have challenged the classic notion that motor learning arises solely from the errors produced during a task, suggesting instead that explicit cognitive strategies can act in concert with the implicit, error\"based, motor learning component. Here, we show that the earliest wave of directionally-tuned neuromuscular activity that occurs within ~100 ms of peripheral visual stimulus onset is selectively influenced by the implicit component of motor learning. In contrast, the voluntary neuromuscular activity associated with reach initiation, which evolves ~100 to 200 ms later is influenced by both the implicit and explicit components of motor learning. The selective influence of the implicit, but not explicit, component of motor learning on the earliest cascade of neuromuscular activity supports the notion that these components of motor learning can differentially influence descending motor pathways.

neuroscience↗

bioRxiv2018

ATRAID, a genetic factor that regulates the clinical action of nitrogen-containing bisphosphonates on bone.

Nitrogen-containing bisphosphonates (N-BPs), such as alendronate, are the most widely prescribed medications for diseases involving bone, with nearly 200 million prescriptions written annually. Recently, widespread use of N-BPs has been challenged due to the risk of rare but traumatic side effects such as atypical femoral fracture (AFFs) and osteonecrosis of the jaw (ONJ). N-BPs bind to and inhibit farnesyl diphosphate synthase (FDPS), resulting in defects in protein prenylation. Yet it remains poorly understood what other cellular factors might allow N-BPs to exert their pharmacological effects. Here, we performed genome-wide studies in cells and patients to identify the poorly characterized gene, ATRAID. Loss of ATRAID function results in selective resistance to N-BP-mediated loss of cell viability and the prevention of alendronate-mediated inhibition of prenylation. ATRAID is required for alendronate inhibition of osteoclast function, and ATRAID-deficient mice have impaired therapeutic responses to alendronate in both postmenopausal and senile (old age) osteoporosis models. Lastly, we performed exome sequencing on patients taking N-BPs that suffered ONJ or an AFF. ATRAID is one of three genes that contain rare non-synonymous coding variants in patients with ONJ or AFF that is also differentially expressed in poor outcome groups of patients treated with N-BPs. We functionally validated this patient variation in ATRAID as conferring cellular hypersensitivity to N-BPs. Our work adds key insight into the mechanistic action of N-BPs and the processes that might underlie differential responsiveness to N-BPs in people. One Sentence SummaryATRAID is essential for responses to the commonly prescribed osteoporosis drugs nitrogen-containing bisphosphonates. OverlineBONE

genomics↗

bioRxiv2018

Single-Cell RNA-seq Reveals a Subpopulation of Cells Underlying β Cell Expansion in the Postnatal Islets

Pancreatic {beta} cells undergo significant expansion and maturation during human and rodent postnatal development. Here, we used single-cell RNA-seq to characterize gene expression patterns at various stages of mouse islet cell development and uncovered a population of cells that is most abundant during the early postnatal period. This cell population lacks expression of FLTP and expresses PDGF receptors. Each of these conditions have previously been associated with proliferative capacity in {beta} cells suggesting that we have identified the proliferative competent of {beta} cell mass expansion. The subpopulation co-express many endocrine lineage-specific genes and exhibits a downregulation of genes associated with mitochondrial oxidative phosphorylation and global protein synthesis. It has upregulated activity of genes in the Wnt, Hippo, PDGF, and Notch pathways and has a significantly higher proliferation potential than the more mature {beta} population. We show that activity of the Notch pathway is required in postnatal {beta} cell expansion where it serves to maintain an undifferentiated endocrine state in the polyhormonal cell population. Collectively, our study identifies a proliferative, progenitor-like cell subpopulation in the postnatal islet as the source of postnatal {beta} cell expansion.

developmental biology↗

bioRxiv2017

Evaluating a sepsis prediction machine learning algorithm using minimal electronic health record data in the emergency department and intensive care unit

IntroductionSepsis is a major health crisis in US hospitals, and several clinical identification systems have been designed to help care providers with early diagnosis of sepsis. However, many of these systems demonstrate low specificity or sensitivity, which limits their clinical utility. We evaluate the effects of a machine learning algodiagnostic (MLA) sepsis prediction and detection system using a before-and-after clinical study performed at Cabell Huntington Hospital (CHH) in Huntington, West Virginia. Prior to this study, CHH utilized the St. Johns Sepsis Agent (SJSA) as a rules-based sepsis detection system.\n\nMethodsThe Predictive algoRithm for EValuation and Intervention in SEpsis (PREVISE) study was carried out between July 1, 2017 and August 30, 2017. All patients over the age of 18 who were admitted to the emergency department or intensive care units at CHH were monitored during the study. We assessed pre-implementation baseline metrics during the month of July, 2017, when the SJSA was active. During implementation in the month of August, 2017, SJSA and the MLA concurrently monitored patients for sepsis risk. At the conclusion of the study period, the primary outcome of sepsis-related in-hospital mortality and secondary outcome of sepsis-related hospital length of stay were compared between the two groups.\n\nResultsSepsis-related in-hospital mortality decreased from 3.97% to 2.64%, a 33.5% relative decrease (P = 0.038), and sepsis-related length of stay decreased from 2.99 days in the pre-implementation phase to 2.48 days in the post-implementation phase, a 17.1% relative reduction (P < 0.001).\n\nConclusionReductions in patient mortality and length-of-stay were observed with use of a machine learning algorithm for early sepsis detection in the emergency department and intensive care units at Cabell Huntington Hospital, and may present a method for improving patient outcomes.\n\nTrial RegistrationClinicalTrials.gov, NCT03235193, retrospectively registered on July 27th 2017.

clinical trials↗

bioRxiv2017

Done in 100 ms: Path-dependent visuomotor transformation in the human upper limb

A core assumption underlying mental chronometry is that more complex tasks increase cortical processing, prolonging reaction times. Here we show that increases in task complexity alter the magnitude, rather than the latency, of the output for a circuit that rapidly transforms visual information into motor actions. We quantified visual stimulus-locked responses (SLRs), which are changes in upper limb muscle recruitment that evolve at a fixed latency [~]100 ms after novel visual stimulus onset. First, we studied the underlying reference frame of the SLR, by dissociating initial eye and hand position. Despite its quick latency, we found that the SLR was expressed in a hand-centric reference frame, suggesting that the circuit mediating the SLR integrated retinotopic visual information with body configuration. Next, we studied the influence of planned movement trajectory, requiring participants to prepare and generate curved or straight reaches in the presence of obstacles to attain the same visual stimulus. We found that SLR magnitude reflected the initial planned movement trajectory, regardless of the ensuing movement curvature. Based on these results, we suggest that the circuit mediating the SLR lies in parallel to other well-studied corticospinal pathways. Although the fixed latency of the SLR precludes extensive cortical processing, inputs conveying information relating to task complexity, such as body configuration and planned movement trajectory, can pre-set nodes within the circuit underlying to the SLR to modulate its magnitude.\n\nSIGNIFICANCE STATEMENTA core assumption underlying mental chronometry is that more complex tasks increase cortical processing, prolonging reaction times. Here, we showed that increases in task complexity altered the magnitude, rather than the latency, of a circuit that rapidly transforms visual information into motor actions. We focus on stimulus-locked responses (SLRs), which are changes in upper limb muscle recruitment that evolve at a fixed latency [~]100 ms after novel visual stimulus onset. We showed that despite is quick latency, the circuitry mediating the SLR transformed a retinotopic visual signal into a hand-centric motor command suitable to contribute to the initial movement trajectory. We suggest that this circuit lies in parallel to other well-studied corticospinal pathways.

neuroscience↗

bioRxiv2016

DNA Methylation Landscape Reflects the Spatial Organization of Chromatin in Different Cells

The relation between DNA methylation and chromatin structure is still largely unknown. By analyzing a large set of sequencing data, we observed a long-range power law correlation of DNA methylation with cell-class-specific scaling exponents in the range of thousands to millions of base pairs. We showed such cell-class-specific scaling exponents are caused by different patchiness of DNA methylation in different cells. By modeling the chromatin structure using Hi-C data and mapping the methylation level onto the modeled structure, we demonstrated the patchiness of DNA methylation is related to chromatin structure. The scaling exponents of the power law correlation is thus a display of the spatial organization of chromatin. Besides, the local correlation of DNA methylation is associated with nucleosome positioning and different between partially-methylated-domain and non-partially-methylated-domain, suggesting their different chromatin structures at several nucleosomes level. Our study provides a novel view of the spatial organization of chromatin structure from a perspective of DNA methylation, in which both long-range and local correlations of DNA methylation along the genome reflect the spatial organization of chromatin.

biophysics↗