Biology subjects

Zeng, H.

Publications and source records attributed to Zeng, H..

At least 181 records · Page 10Linked to original sources

bioRxiv2020

Therapeutic Drugs Targeting 2019-nCoV Main Protease by High-Throughput Screening

2019 Novel Coronavirus (2019-nCoV) is a virus identified as the cause of the outbreak of pneumonia first detected in Wuhan, China. Investigations on the transmissibility, severity, and other features associated with this virus are ongoing. Currently, there is no vaccine or therapeutic antibody to prevent the infection, and more time is required to develop an effective immune strategy against the pathogen. In contrast, specific inhibitors targeting the key protease involved in replication and proliferation of the virus are the most effective means to alleviate the epidemic. The main protease of SARS-CoV is essential for the life cycle of the virus, which showed 96.1% of similarity with the main proteaseof 2019-nCoV, is considered to be an attractive target for drug development. In this study, we have identified 4 small molecular drugs with high binding capacity with SARS-CoV main protease by high-throughput screening based on the 8,000 clinical drug libraries, all these drugs have been widely used in clinical applications with guaranteed safety, which may serve as promising candidates to treat the infection of 2019-nCoV.

pharmacology and toxicology↗

bioRxiv2020

Alterations of human lung and gut microbiome in non-small cell lung carcinomas and distant metastasis

BackgroundNon-small cell lung cancer (NSCLC) is the leading cause of cancer-related deaths worldwide. Although dysbiosis of lung and gut microbiota have been associated with NSCLC, their relative contributions are unclear; in addition, their roles in distant metastasis (DM) are still illusive. ResultsWe surveyed the fecal and sputum (as a proxy for lung) microbiota in healthy controls and NSCLC patients of various stages, and found significant perturbations of gut- and sputum-microbiota in patients with NSCLC and DM. Machine-learning models combining both microbiota (mixed models) performed better than either dataset in patient stratification, with the highest area under the curve (AUC) value of 0.842. Sputum-microbiota contributed more than the gut in the mixed models; in addition, sputum-only models performed similarly to the mixed models in most cases. Several microbial-biomarkers were shared by both microbiota, indicating their similar roles at distinct body sites. Microbial-biomarkers of distinct disease stages were mostly shared, suggesting biomarkers for distant metastasis could be acquired early. Furthermore, Pseudomonas aeruginosa, a species previously associated with wound infections, was significantly more abundant in brain metastasis, indicating distinct types of DMs could have different microbial-biomarkers. ConclusionOur results indicate that alterations of sputum-microbiota have stronger relationships with NSCLC and distant metastasis than the gut, and strongly support the feasibility of metagenome-based non-invasive disease diagnosis and risk evaluation.

microbiology↗

bioRxiv2019

The spatial structure of feedforward information in mouse primary visual cortex

Location-sensitive and motion-sensitive units are the two major functional types of feedforward projections from lateral genicular nucleus (LGN) to primary visual cortex (V1) in mouse. The distribution of these inputs in cortical depth remains under debate. By measuring the calcium activities of LGN axons in V1 of awake mice, we systematically mapped their functional and structural properties. Although both types distributed evenly across cortical depth, we found that they differ significantly across multiple modalities. Compared to the location-sensitive axons, which possessed confined spatial receptive fields, the motion-sensitive axons lacked spatial receptive fields, preferred lower temporal, higher spatial frequencies and had wider horizontal bouton spread. Furthermore, the motion-sensitive axons showed a strong depth-dependent motion direction bias while the location-sensitive axons showed a depth-independent OFF dominance. Overall, our results suggest a new model of receptive biases and laminar structure of thalamic inputs to V1. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=177 SRC="FIGDIR/small/888156v2_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@35c887org.highwire.dtl.DTLVardef@1001d54org.highwire.dtl.DTLVardef@8585b2org.highwire.dtl.DTLVardef@c8a35_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2019

Distribution and strength of interlaminar synaptic connectivity in mouse primary visual cortex revealed by two-photon optogenetic stimulation

The most common synaptic connections between neurons in different cortical layers form the basis of the canonical cortical microcircuit. Understanding of cortical function will require further development and application of methods to efficiently characterize synaptic connections within and outside of the canonical pathway. Accordingly, we measured synaptic inputs onto superficial excitatory neurons in response to sequential two-photon optogenetic stimulation of neurons in deeper layers. Layer 4 excitatory neurons and somatostatin-neurons within layer 2/3 represented the most common sources of input. Although connections from excitatory and somatostatin-neurons in layer 5 were less common, the amplitudes of synaptic responses were equally strong. We examined synaptic strength across all connections, as well as the relationships between the strength of connections diverging from a common presynaptic neuron or converging to a single target. While the overall distribution indicates synaptic weight is concentrated to a few connections, strong excitatory connections are distributed across cells.

neuroscience↗

bioRxiv2019

Distinct transcriptomic cell types and neural circuits of the subiculum and prosubiculum along the dorsal-ventral axis

Subicular region plays important roles in spatial processing and many cognitive functions and these were mainly attributed to subiculum (Sub) rather than prosubiculum (PS). Using single-cell RNA-sequencing (scRNA-seq) technique we have identified up to 27 distinct transcriptomic clusters/cell types, which were registered to anatomical sub-domains in Sub and PS. Based on reliable molecular markers derived from transcriptomic clustering and in situ hybridization data, the precise boundaries of Sub and PS have been consistently defined along the dorsoventral (DV) axis. Using these borders to evaluate Cre-line specificity and tracer injections, we have found bona fide Sub projections topographically to structures important for spatial processing and navigation. In contrast, PS along DV axis sends its outputs to widespread brain regions crucial for motivation, emotion, reward, stress, anxiety and fear. Brain-wide cell-type specific projections of Sub and PS have also been revealed using specific Cre-lines. These results reveal two molecularly and anatomically distinct circuits centered in Sub and PS, respectively, providing a consistent explanation to historical data and a clearer foundation for future functional studies. HighlightsO_LI27 transcriptomic cell types identified in and spatially registered to "subicular" regions. C_LIO_LIAnatomic borders of "subicular" regions reliably determined along dorsal-ventral axis. C_LIO_LIDistinct cell types and circuits of full-length subiculum (Sub) and prosubiculum (PS). C_LIO_LIBrain-wide cell-type specific projections of Sub and PS revealed with specific Cre-lines. C_LI In BriefDing et al. show that mouse subiculum and prosubiculum are two distinct regions with differential transcriptomic cell types, subtypes, neural circuits and functional correlation. The former has obvious topographic projections to its main targets while the latter exhibits widespread projections to many subcortical regions associated with reward, emotion, stress and motivation.

neuroscience↗

bioRxiv2019

Large-scale Analysis of 2,152 dataset reveals key features of B cell biology and the antibody repertoire

Antibody repertoire sequencing (Ig-seq) has been widely used in studying humoral responses, with promising results. However, the promise of Ig-seq has not yet been fully realized, and key features of the antibody repertoire remain elusive or controversial. To clarify these key features, we analyzed 2,152 high-quality heavy chain antibody repertoires, representing 582 donors and a total of 360 million clones. Our study revealed that individuals exhibit very similar gene usage patterns for germline V, D, and J genes and that 53 core V genes contribute to more than 99% of the heavy chain repertoire. We further found that genetic background is sufficient but not necessary to determine usage of V, D, and J genes. Although gene usage pattern is not affected by age, we observed a significant sex preference for 24 V genes, 9 D genes and 5 J genes, but found no positional bias for V-D and D-J recombination. In addition, we found that the number of observed clones that were shared between any two repertoires followed a linear model and noted that the mutability of hot/cold spots and single nucleotides within antibody genes suggested a strand-specific somatic hypermutation mechanism. This population-level analysis resolves some critical characteristics of the antibody repertoire and thus may serve as a reference for research aiming to unravel B cell-related biology or diseases. The metrics revealed here will be of significant value to the large cadre of scientists who study the antibody repertoire.

immunology↗

bioRxiv2019

Real-time Continuous Hand Motion Myoelectric Decoding by Automated Data Labeling

In this paper an automated data labeling (ADL) neural network was proposed to streamline dataset collecting for real-time predicting the continuous motion of hand and wrist, these gestures are only decoded from a surface electromyography (sEMG) array of eight channels. Unlike collecting both the bio-signals and hand motion signals as samples and labels in supervised learning, this algorithm only collects the unlabeled sEMG into an unsupervised neural network, in which the hand motion labels are auto-generated. The coefficient of determination (r2) for three DOFs, i.e. wrist flex/extension, wrist pro/supination, hand open/close, was 0.86, and 0.87 respectively. The comparison between real motion labels and auto-generated labels shows that the latter has earlier response than former. The results of Fitts law test indicate that ADL has capability of controlling multi-DOFs simultaneously even though the training set only contains sEMG data from single DOF gesture. Moreover, no more hand motion measurement needed which greatly helps upper-limb amputee imagine the gesture of residual limb to control a dexterous prosthesis.

bioengineering↗

bioRxiv2019

On the correspondence of electrical and optical physiology in in vivo population-scale two-photon calcium imaging.

Multiphoton calcium imaging is commonly used to monitor the spiking of large populations of neurons. Recovering action potentials from fluorescence necessitates calibration experiments, often with simultaneous imaging and cell-attached recording. Here we performed calibration for imaging conditions matching those of the Allen Brain Observatory. We developed a novel crowd-sourced, algorithmic approach to quality control. Our final data set was 50 recordings from 35 neurons in 3 mouse lines. Our calibration indicated that 3 or more spikes were required to produce consistent changes in fluorescence. Moreover, neither a simple linear model nor a more complex biophysical model accurately predicted fluorescence for small numbers of spikes (1-3). We observed increases in fluorescence corresponding to prolonged depolarizations, particularly in Emx1-IRES-Cre mouse line crosses. Our results indicate that deriving spike times from fluorescence measurements may be an intractable problem in some mouse lines.

neuroscience↗

bioRxiv2019

Relationship between spiking activity and simultaneously recorded fluorescence signals in transgenic mice expressing GCaMP6

Two-photon calcium imaging is often used with genetically encoded calcium indicators (GECIs) to investigate neural dynamics, but the relationship between fluorescence and action potentials (spikes) remains unclear. Pioneering work linked electrophysiology and calcium imaging in vivo with viral GECI expression, albeit in a small number of cells. Here we characterized the spikefluorescence transfer function in vivo of 91 layer 2/3 pyramidal neurons in primary visual cortex in four transgenic mouse lines expressing GCaMP6s or GCaMP6f. We found that GCaMP6s cells have spike-triggered fluorescence responses of larger amplitude, lower variability and greater single-spike detectability than GCaMP6f. Mean single-spike detection rates at high spatiotemporal resolution measured in our data was >70% for GCaMP6s and ~40-50% for GCaMP6f (at 5% false positive rate). These rates are estimated to decrease to 25-35% for GCaMP6f under generally used population imaging conditions. Our ground-truth dataset thus supports more refined inference of neuronal activity from calcium imaging.

neuroscience↗

bioRxiv2019

Lyb-2-4, a unique genomic region of hypervirulent carbapenem-resistant Acinetobacter baumannii

Acinetobacter baumannii is an important human pathogen due to its multi-drug resistance, but is usually with low-grade virulence. Although a mouse model revealed different virulence grades of clinical carbapenem-resistant A. baumannii (CRAB) strains, the genetic basis remains unknown. We collected 61 CRAB isolates from intensive care unit of Shenzhen Peoples Hospital (Shenzhen, China), and analyzed them used whole genome sequencing (WGS), multilocus sequence typing (MLST) and core genome MLST (cgMLST), transmission chain reconstruction and Comparative genomic tools. A mouse pneumonia model was used to confirm the hypervirulent phenotype. Eleven complex types (CT) were identified based on core genome multilocus sequence typing scheme. CT512 showed higher transmissibility and bloodstream infection rates than other CTs. A genomic region Lyb-2-4 was shared by CT512 and CT2092 but not CT2085. The mortality rates of patient infected with CRAB harboring Lyb-2-4 was significantly higher than those infected with CRAB isolates without Lyb-2-4 (77.8% vs 24.5%, p < 0.01). In the mouse model, the survival rates of strains containing the Lyb-2-4 region (LAC-4, 5122 and 2092) were significantly lower than for strains without Lyb-2-4 (7152, 71517, 20859 and ATCC17978). One open reading frame (ORF) was a marker for the presence of Lyb-2-4, and PCR of a segment of this ORF, designated as hvcT, served as a tag for hypervirulent CRAB. Our study should be very useful in advising the clinician to implement medical intervention earlier, and also making the worldwide surveillance of these hypervirulent CRAB strains easier.\n\nIMPORTANCEHypervirulent CRAB strains are expected to pose a threat to human health because infection of these strains is associated with high mortality and multidrug resistance. The rapid hypervirulent CRAB identification assay will facilitate prompt medical intervention. Our findings should provoke surveillance for hypervirulent CRAB strains harboring Lyb-2-4 in other countries. Further research should focus on the mechanism of hypervirulence, the acquisition of this genomic region and the development of control measures to prevent further dissemination.

microbiology↗

bioRxiv2019

A bestiary of genetic mouse lines and related tools for inducible and reversible intersectional misexpression

Thanks to many advances in genetic manipulation, mouse models have become very powerful in their ability to interrogate biological processes. In order to precisely target expression of a gene of interest to particular cell types, intersectional genetic approaches utilizing two promoter/enhancers unique to a cell type are ideal. Within these methodologies, variants that add temporal control of gene expression are the most powerful. We describe the development, validation and application of an intersectional approach that involves three transgenes, requiring the intersection of two promoter/enhancers to target gene expression to precise cell types. Furthermore, the approach utilizes available lines expressing tTA/rTA to control timing of gene expression based on whether doxycycline is absent or present, respectively. We also show that the approach can be extended to other animal models, using chicken embryos. We generated three mouse lines targeted at the Tigre (Igs7) locus with TRE-loxP-tdTomato-loxP upstream of three genes (p21, DTA and Ctgf) and combined them with Cre and tTA/rtTA lines that target expression to the cerebellum and limbs. Our tools will facilitate unraveling biological questions in multiple fields and organisms. Summary statementAhmadzadeh et al. present a collection of four mouse lines and genetic tools for misexpression-mediated manipulation of cellular activity with high spatiotemporal control, in a reversible manner.

molecular biology↗

bioRxiv2019

Improvising at Rest: Differentiating Jazz and Classical Music Training with Resting State Functional Connectivity

Jazz improvisation offers a model for creative cognition, as it involves the real-time creation of a novel, information-rich product. Previous research has shown that when musicians improvise, they recruit regions in the Default Mode Network (DMN) and Executive Control Network (ECN). Here, we ask whether these findings from task-fMRI studies might extend to intrinsic differences in resting state functional connectivity. We compared Improvising musicians, Classical musicians, and Minimally Musically Trained (MMT) controls in seed-based functional connectivity and network analyses in resting state functional MRI. We also examined the functional correlates of behavioral performance in musical improvisation and divergent thinking. Seed-based analysis consistently showed higher connectivity in ventral DMN (vDMN) and bilateral ECN in both groups of musically trained individuals as compared to MMT controls, with additional group differences in primary visual network, precuneus network, and posterior salience network. In particular, primary visual network connectivity to DMN and ECN was highest in Improvisational musicians, whereas within-network connectivity of vDMN and precuneus network was higher in both Improvisational and Classical musicians than in MMT controls; in contrast, connectivity between posterior salience network and superior parietal lobule was highest in Classical musicians. Furthermore, graph-theoretical analysis indicated heightened betweenness centrality, clustering, and local efficiency in Classical musicians. Taken together, results suggest that heightened functional connectivity among musicians can be explained by higher within-network connectivity (more tight-knit cortical networks) in Classical musicians, as opposed to more disperse, globally-connected cortical networks in Improvisational musicians.\n\nHighlightsO_LIMusic training is associated with higher resting state connectivity\nC_LIO_LIHigher connectivity in Improvisational musicians from visual network to ECN and DMN\nC_LIO_LIClassical musicians show higher vDMN and Precuneus within-network connectivity\nC_LIO_LIImprovisation and divergent thinking performance correlate with similar connectivity patterns\nC_LI

neuroscience↗

bioRxiv2019

HIPK4 is essential for murine spermiogenesis

Mammalian spermiogenesis is a remarkable cellular transformation, during which round spermatids elongate into chromatin-condensed spermatozoa. The signaling pathways that coordinate this process are not well understood, and we demonstrate here that homeodomain-interacting protein kinase 4 (HIPK4) is essential for spermiogenesis and male fertility in mice. HIPK4 is predominantly expressed in round and early elongating spermatids, and Hipk4 knockout males are sterile, exhibiting phenotypes consistent with oligoasthenoteratozoospermia. Hipk4 mutant sperm have reduced oocyte binding and are incompetent for in vitro fertilization, but they can still produce viable offspring via intracytoplasmic sperm injection. Ultrastructural analyses of HIPK4-null male germ cells reveal defects in the filamentous actin (F-actin)-scaffolded acroplaxome during spermatid elongation and abnormal head morphologies in mature spermatozoa. We further observe that HIPK4 overexpression induces branched F-actin structures in cultured fibroblasts, supporting a role for this kinase in cytoskeleton remodeling. Our findings establish HIPK4 as an essential regulator of sperm head shaping and potential target for male contraception.

developmental biology↗

bioRxiv2019

Antibody Complementarity Determining Region Design Using High-Capacity Machine Learning

The precise targeting of antibodies and other protein therapeutics is required for their proper function and the elimination of deleterious off-target effects. Often the molecular structure of a therapeutic target is unknown and randomized methods are used to design antibodies without a model that relates antibody sequence to desired properties. Here we present a machine learning method that can design human Immunoglobulin G (IgG) antibodies with target affinities that are superior to candidates from phage display panning experiments within a limited design budget. We also demonstrate that machine learning can improve target-specificity by the modular composition of models from different experimental campaigns, enabling a new integrative approach to improving target specificity. Our results suggest a new path for the discovery of therapeutic molecules by demonstrating that predictive and differentiable models of antibody binding can be learned from high-throughput experimental data without the need for target structural data.\n\nSignificanceAntibody based therapeutics must meet both affinity and specificity metrics, and existing in vitro methods for meeting these metrics are based upon randomization and empirical testing. We demonstrate that with sufficient target-specific training data machine learning can suggest novel antibody variable domain sequences that are superior to those observed during training. Our machine learning method does not require any target structural information. We further show that data from disparate antibody campaigns can be combined by machine learning to improve antibody specificity.

immunology↗

bioRxiv2019

Complete single neuron reconstruction reveals morphological diversity in molecularly defined claustral and cortical neuron types

Ever since the seminal findings of Ramon y Cajal, dendritic and axonal morphology has been recognized as a defining feature of neuronal types. Yet our knowledge concerning the diversity of neuronal morphologies, in particular distal axonal projection patterns, is extremely limited. To systematically obtain single neuron full morphology on a brain-wide scale, we established a platform with five major components: sparse labeling, whole-brain imaging, reconstruction, registration, and classification. We achieved sparse, robust and consistent fluorescent labeling of a wide range of neuronal types by combining transgenic or viral Cre delivery with novel transgenic reporter lines. We acquired high-resolution whole-brain fluorescent images from a large set of sparsely labeled brains using fluorescence micro-optical sectioning tomography (fMOST). We developed a set of software tools for efficient large-volume image data processing, registration to the Allen Mouse Brain Common Coordinate Framework (CCF), and computer-assisted morphological reconstruction. We reconstructed and analyzed the complete morphologies of 1,708 neurons from the striatum, thalamus, cortex and claustrum. Finally, we classified these cells into multiple morphological and projection types and identified a set of region-specific organizational rules of long-range axonal projections at the single cell level. Specifically, different neuron types from different regions follow highly distinct rules in convergent or divergent projection, feedforward or feedback axon termination patterns, and between-cell homogeneity or heterogeneity. Major molecularly defined classes or types of neurons have correspondingly distinct morphological and projection patterns, however, we also identify further remarkably extensive morphological and projection diversity at more fine-grained levels within the major types that cannot presently be accounted for by preexisting transcriptomic subtypes. These insights reinforce the importance of full morphological characterization of brain cell types and suggest a plethora of ways different cell types and individual neurons may contribute to the function of their respective circuits.

neuroscience↗

bioRxiv2019

Entecavir resistance mutations rtL180M/T184L/M204V combined with rtA200V lead to tenofovir resistance

Background & AimsTenofovir disoproxil fumarate (TDF) imposes a high genetic barrier to drug resistance and potently inhibits replication of multidrug-resistant hepatitis B virus (MDR HBV) and few clinical cases with confirmed TDF-resistance have been reported to date. We reported a quadruple mutant which showed moderate resistant to TDF.\n\nMethods and resultsViral rebound was reported in a patient with chronic hepatitis B who underwent TDF monotherapy and harbored a quadruple mutant consisting of classic ETV-resistance mutations (rtL180M/T184L/M204V) together with an rtA200V mutation in the reverse transcriptase gene. Sequencing analysis revealed that this quadruple mutant emerged as a major viral population. In vitro phenotyping demonstrated that the rtL180M/T184L/A200V/M204V mutant had moderate resistance to TDF treatment, with a 4.52-fold higher half maximal effective concentration than that of wild-type virus. Importantly, this patient with TDF resistance achieved virological suppression after TDF/ETV combination rescue therapy.\n\nConclusionAn rtL180M/T184L/A200V/M204V mutant with moderate resistance to TDF monotherapy was selected during sequential NA treatment in a stepwise manner. ETV/TDF combination therapy effectively suppressed replication of this TDF resistant mutant. Our studies provide novel insights into the treatment of NA-naive patients as well as patients with TDF resistance.

microbiology↗

bioRxiv2019

TeraVR Empowers Precise Reconstruction of Complete 3-D Neuronal Morphology in the Whole Brain

Neuron morphology is recognized as a key determinant of cell type, yet the quantitative profiling of a mammalian neurons complete three-dimensional (3-D) morphology remains arduous when the neuron has complex arborization and long projection. Whole-brain reconstruction of neuron morphology is even more challenging as it involves processing tens of teravoxels of imaging data. Validating such reconstructions is extremely laborious. We developed TeraVR, an open-source virtual reality annotation system, to address these challenges. TeraVR integrates immersive and collaborative 3-D visualization, interaction, and hierarchical streaming of teravoxel-scale images. Using TeraVR, we produced precise 3-D full morphology of long-projecting neurons in whole mouse brains and developed a collaborative workflow for highly accurate neuronal reconstruction.

neuroscience↗

bioRxiv2019

Epigenetic landscape and AAV targeting of human neocortical cell classes

Viral genetic tools to target specific brain cell types in humans and non-genetic model organisms will transform basic neuroscience and targeted gene therapy. Here we used comparative epigenetics to identify thousands of human neuronal subclass-specific putative enhancers to regulate viral tools, and 34% of these were conserved in mouse. We established an AAV platform to evaluate cellular specificity of functional enhancers by multiplexed fluorescent in situ hybridization (FISH) and single cell RNA sequencing. Initial testing in mouse neocortex yields a functional enhancer discovery success rate of over 30%. We identify enhancers with specificity for excitatory and inhibitory classes and subclasses including PVALB, LAMP5, and VIP/LAMP5 cells, some of which maintain specificity in vivo or ex vivo in monkey and human neocortex. Finally, functional enhancers can be proximal or distal to cellular marker genes, conserved or divergent across species, and could yield brain-wide specificity greater than the most selective marker genes.

neuroscience↗