Biology subjects

Zhou, S.

Publications and source records attributed to Zhou, S..

At least 181 records · Page 10Linked to original sources

bioRxiv2022

Multiplexing working memory and time: encoding retrospective and prospective information in neural trajectories

Working memory (WM) and timing are generally considered distinct cognitive functions, but similar neural signatures have been implicated in both. To explore the hypothesis that WM and timing may rely on shared neural mechanisms, we used psychophysical tasks that contained either task-irrelevant timing or WM components. In both cases the task-irrelevant component influenced performance. RNN simulations revealed that cue-specific neural sequences, which multiplexed WM and time, emerged as the dominant regime that captured the behavioral findings. Over the course of training RNN dynamics transitioned from low-dimensional ramps to high-dimensional neural sequences, and depending on task requirements, steady-state or ramping activity was also observed. Analysis of RNN structure revealed that neural sequences relied primarily on inhibitory connections, and could survive the deletion of all excitatory-to- excitatory connections. Our results suggest that in some instances WM is encoded in time-varying neural activity because of the importance of predicting when WM will be used.

neuroscience↗

bioRxiv2022

Segmental flexibility of bispecific T-cell engagers regulates the dynamics of immune synapse formation

Bispecific T-cell engagers (TcEs) link T cell receptors to tumor-associated antigens on cancer cells, forming cytotoxic immunological synapses (IS). Close membrane-to-membrane contact ([≤]13 nm) has been proposed as a key mechanism of TcE function. To investigate this and identify potential additional mechanisms, we compared four immunoglobulin G1-based (IgG1) TcE Formats (A-D) targeting CD3{varepsilon} and Her2, designed to create varying intermembrane distances (A B=C>D. In a minimal system for IS formation on SLBs, TcE performance followed the trend A=B=C>D. Addition of close-contact requiring CD58 co-stimulation revealed phospholipase C-{gamma} activation matching cytotoxicity with A>B=C>D. Our findings suggest that, when adhesion is equivalent, TcE potency is determined by two parameters: contact distance and flexibility. Both the close/far-contact formation axis and the low/high flexibility axis significantly impact TcE potency, explaining the similar potency of Format B (close-contact/high flexibility) and C (far-contact/low flexibility). Significance statementBispecific T-cell engagers (TcEs) are immunotherapeutic drugs that trigger the destruction of cancer cells by linking T cells to cancer cell through specific surface molecules (antigens). We designed a series of TcEs with varying distances between their binding sites and flexibilities of the TcE-antigen complexes. By combining structural and functional analyses, we confirmed close-contact formation between T cells and cancer cells as a critical determinant, mediated by co-activating receptors. Furthermore, we also identified molecular flexibility of the TcE-antigen complex as a further critical parameter for TcE potency. These findings provide novel insights into TcE function and highlight the importance of both parameters for future research and the design of improved immunotherapies.

immunology↗

bioRxiv2022

Two Rac1 pools integrate the direction and coordination of collective cell migration

Integration of collective cell direction and coordination is believed to ensure collective guidance for efficient movement. Previous studies demonstrated that chemokine receptors PVR and EGFR govern a gradient of Rac1 activity essential for collective guidance of Drosophila border cells, whose mechanistic insight is unknown. By monitoring and manipulating subcellular Rac1 activity, here we reveal two switchable Rac1 pools at border cell protrusions and supracellular cables, two important structures responsible for direction and coordination. Rac1 and Rho1 form a positive feedback loop that guides mechanical coupling at cables to achieve migration coordination. Rac1 cooperates with Cdc42 to control protrusion growth for migration direction, as well as to regulate the protrusion-cable exchange, linking direction and coordination. PVR and EGFR guide correct Rac1 activity distribution at protrusions and cables. Therefore, our studies emphasize the existence of a balance between two Rac1 pools, rather than a Rac1 activity gradient, as an integrator for the direction and coordination of collective cell migration.

cell biology↗

bioRxiv2022

Benzo(a)pyrene regulates chaperone-mediated autophagy via heat shock protein 90

The Benzo(a)pyrene (Bap) exposure induced oxidative damage, DNA damage and autophagy. To explore the molecular mechanism of BaP-induced autophagy. In these studies, we first found that heat shock protein 90 (HSP90), heat shock cognate 70 (HSC70) and lysosomal-associated membrane protein type 2 receptor (Lamp-2a) expressions of C57BL mice lung tissue and A549 cells exposed to BaP were significant increase, as well as Bap induced DNA double-strand breaks (DSBs) and activated DNA damage responses, as evidenced by comet assay and {gamma}-H2AX foci analysis in A549 cells. Our results demonstrated BaP induced CMA and caused DNA damage. Next, we knocked down HSP90 expression by the HSP90 Inhibitor, NVP-AUY 922, exposed or HSP90 shRNA lentivirus transduction in A549 cells. HSC70 and Lamp-2a expressions of these cells exposed to BaP were not significant increase, which showed that BaP inducted CMA was mediated by HSP90. Further, HSP90 shRNA prevented BaP induced of Bap which suggested BaP regulated CMA and caused DNA damage by HSP90. Our results elucidated a new mechanism of BaP regulated CMA through HSP90.

biochemistry↗

bioRxiv2022

Strength of selection potentiates distinct adaptive responses in an evolution experiment with outcrossing yeast

Experimental evolution studies with sexually-reproducing populations consistently find that adaptation is highly polygenic and fueled by standing genetic variation. However, studies vary substantially with respect to other evolutionary dynamics. Resolving these discrepancies is a crucial next step as we move toward extrapolating findings from laboratory systems to natural populations. Differences in experimental parameters between studies can perhaps answer these questions, and here we assess how one such parameter - selection intensity - influences outcomes. We subject populations of outcrossing Saccharomyces cerevisiae to zero, moderate, and high ethanol stress for [~]200 generations and ask: 1) does stronger selection lead to greater changes in allele frequencies at adaptive sites; and 2) do targets of selection vary with intensity? With respects to sites with large effects, we find some evidence for positive correlations between selection intensity and allele frequency change. While we observe shared genomic responses across treatments, we also identify treatment-specific responses. Combined with evidence of phenotypic trade-offs between treatments, our findings support the hypothesis that selection intensity influences evolutionary outcomes due to pleiotropic and epistatic interactions. We conclude that it should be a major consideration when attempting to generalize inferences across studies; in other words, we argue that different intensities of selection effectively create distinct environments and genotype-by-environment interactions. Lastly, our results demonstrate the importance of clearly-defined controls in experimental evolution. Despite working with a presumably lab-adapted model system, without this element we would not have been able to distinguish genomic responses to ethanol stress from those associated with laboratory conditions.

evolutionary biology↗

bioRxiv2022

Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues

Although the function of tRNA in translational process is well established, it remains controversial whether tRNA abundance is tightly associated with translational efficiency (TE) in mammals. For example, how critically the expression of tRNAs contributes to the establishment of tissue-specific proteomes in mammals has not been well addressed. Here, we measured both tRNA expression using DM-tRNA-seq and ribosome-associated mRNAs in the brain, heart, and testis of RiboTag mice. Remarkable variation in the expression of tRNA isodecoders was observed among the different tissues. When the statistical effect of isodecoder-grouping on reducing variations is considered through permutating the anticodons, we observed an expected reduction in the tissue-variations of anticodon expression, an unexpected smaller variation of anticodon usage bias, and an unexpected larger variation of tRNA isotype expression. Regardless whether or not they share the same anticodons, isotypes encoding the same amino acids are co-expressed across different tissues. Based on the tRNA expression and TE computed from RiboTag-seq, we find that the tRNA adaptation index (tAI) values and TE are significantly correlated in the same tissues but not among tissues; tRNAs and the amino acid compositions of translating peptides are positively correlated in the same tissues but not between tissues. We therefore hypothesize that the tissue-specific expression of tRNAs might be related to post-transcriptional mechanisms, such as aminoacylation, modification, and tRNA-derived small RNAs (tsRNAs). This study provides a resource for tRNA and translation studies to gain novel insights into the dynamics of tRNAs and their role in translational regulation.

cell biology↗

bioRxiv2022

A Fast, Provably Accurate Approximation Algorithm for Sparse Principal Component Analysis Reveals Human Genetic Variation Across the World

Principal component analysis (PCA) is a widely used dimensionality reduction technique in machine learning and multivariate statistics. To improve the interpretability of PCA, various approaches to obtain sparse principal direction loadings have been proposed, which are termed Sparse Principal Component Analysis (SPCA). In this paper, we present ThreSPCA1, a provably accurate algorithm based on thresholding the Singular Value Decomposition for the SPCA problem, without imposing any restrictive assumptions on the input covariance matrix. Our thresholding algorithm is conceptually simple; much faster than current state-of-the-art; and performs well in practice. When applied to genotype data from the 1000 Genomes Project, ThreSPCA is faster than previous benchmarks, at least as accurate, and leads to a set of interpretable biomarkers, revealing genetic diversity across the world.

genomics↗

bioRxiv2022

Single and complex spikes relay distinct frequency-dependent circuit information in the hippocampus

Hippocampal neurons generate either single spikes or stereotyped bursts of spikes known as complex spikes. Although single and complex spikes co-occur in the same neuron, their contribution to information processing remains unclear. We analyzed hippocampal CA1 neurons in awake mice and in behaving rats, combining cellular membrane voltage imaging with optogenetics and extracellular recordings. We found that network-driven subthreshold membrane rhythms in the theta versus gamma frequencies preferably entrained complex versus single spikes in individual neurons. Optogenetic membrane perturbation revealed a causal link between subthreshold theta and gamma power and the initiation of complex versus single spikes. Further, single and complex spikes exhibited different place field properties and frequency-dependent coding during spatial navigation. Thus, individual hippocampal neurons do not integrate theta and gamma rhythms into a combined spike timing code, but instead, transmit frequency-specific information as distinct output modes of single versus complex spikes during spatial cognition.

neuroscience↗

bioRxiv2022

Deep brain stimulation creates information lesion through membrane depolarization

Deep brain stimulation (DBS) is a promising neuromodulation therapy that alters neural activity via intracranial electrical stimulation. However, the neurophysiological mechanisms of DBS remain largely unknown, because of the difficulty of obtaining cellular resolution recordings without electrical interference. Here, we performed high-speed membrane voltage fluorescence imaging of individual hippocampal CA1 neurons during DBS in awake mice. We discovered that DBS, delivered at either 40Hz or 140Hz, reliably depolarizes somatic membrane potentials. Further, DBS enhanced spike rates and paced membrane voltage and spike timing at the stimulation frequency, though more prominent at 40Hz than 140Hz. To determine how DBS induced membrane voltage change impacts neurons ability to process inputs, we optogenetically evoked membrane depolarization. We found that neurons become unreliable in responding to optogenetic inputs during DBS, particularly during 140Hz DBS. These results demonstrate that DBS produces powerful membrane depolarization that interferes with neurons ability to process inputs, creating information lesion.

neuroscience↗

bioRxiv2022

A novel PLS1 c.981+1G>A variant causes autosomal-dominant hereditary hearing loss in a family via up-regulation of the PI3K-Akt signaling pathway

BackgroundThe fimbrin protein family contains a variety of proteins, of which Plastin1 (PLS1) is an important member. The latest researches show that variations in the coding region of PLS1 gene is related to the development of deafness. However, it remains unknown about the molecular mechanism of deafness caused by PLS1 gene variants. Methodswhole exome sequencing was performed on the affected family members and healthy ones to identify the pathogenic variants, followed by sanger sequencing. Minigene assay was conducted to investigate the impact of the variant on PLS1 mRNA splicing. The pathogenicity of the variant was further investigated in zebrafish. RNA-sequencing (RNA-seq) was done for analyzing the dysregulated downstream signaling pathways caused by knockdown of PLS1 expression. ResultsWe identified a novel variant PLS1 c.981+1G>A in a large Chinese family with hearing loss and demonstrated that the variant is responsible for the occurrence of hearing loss by inducing Exon8 skipping or deletion of Exon8 (47bp). The variant caused abnormal inner ear phenotypes, characterized by decreased mean otolith distance, anterior otolith diameter, posterior otolith diameter, and cochlear diameter, swimming speed and distance in zebrafish. Furthermore, silencing PLS1 expression significantly upregulated genes in the PI3K-Akt signaling pathway, including Col6a3, Spp1, Itgb3 and Hgf. ConclusionsPLS1 c.981+1G>A is a novel pathogenic variant for hearing loss by inducing Exon8 skipping or deletion of Exon8 (47bp). Up-regulation of the PI3K-Akt signaling pathway plays an important role in the pathogenesis of PLS-1 gene.

genetics↗

bioRxiv2022

Hand Gesture Prediction via Transient-phase sEMG using Transfer Learning of Dilated Efficient CapsNet: Towards Generalization for Neurorobotics

There has been an accelerated surge to utilize the deep neural network for decoding central and peripheral activations of the humans nervous system to boost up the spatiotemporal resolution of neural interfaces used in neurorobotics. Such algorithmic solutions are motivated for use in human-centered robotic systems, such as neurorehabilitation, prosthetics, and exoskeletons. These methods are proved to achieve higher accuracy on individual data when compared with the conventional machine learning methods but are also challenged by their assumption of having access to massive training samples. ObjectiveIn this letter, we propose Dilated Efficient CapsNet to improve the predictive performance when the available individual data is very minimum and not enough to train an individualized network for controlling a personalized robotic system. MethodWe proposed the concept of transfer learning using a new design of the dilated efficient capsular neural network to relax the need of having access to massive individual data and utilize the field knowledge which can be learned from a group of participants. In addition, instead of using complete sEMG signals, we only use the transient phase, reducing the volume of training samples to 20% of the original and maximizing the agility. ResultsIn experiments, we validate our model performance with various amounts of injected personalized training data (25%-100% of transient phase) that is segmented once by time and once by repetition. The results of this paper support the use of transfer learning using a dilated capsular neural network and show that with the use of such a model, the knowledge domain learned on a small number of subjects can be utilized to minimize the need for new data of new subjects while focusing only on the transient phase of contraction (which is a challenging neural interfacing problem).

bioengineering↗

bioRxiv2022

Structure of IgG-Fc hexamer reveals a mutual lock-and-key mode of Fc-Fc interaction

IgG exists mainly as monomer, but recent studies suggest that IgG forms hexamer to mediate antibody functions. Although many structures of IgG monomer and its fragments are determined, there is no IgG hexamer structure at atomic level due to the weak Fc-Fc interactions. Here we engineered a hexameric IgG with IgM tailpiece fusion and determined the structure by cryo-EM. IgG-Fc hexamer forms hexagon symmetry with the six Fcs lie in a plane with Fc-Fc interaction in a mutual lock-and-key mode. This structure provides structural insights into Fc-Fc interaction of IgG and reveals molecular basis for its function.

biophysics↗

bioRxiv2022

Operational tolerance is early acquired and long maintained in 50% liver allograft transplantation

Lifelong anti-rejection therapy is mandatory to weaken the host immune system and maintain the graft functions after organ transplantation, its toxicities and side-effects incidentally elicit mortalities and morbidities. Operational tolerance is a long immunosuppression-free state in which the allograft functions well and no immunological rejections occur, and no operational tolerance is clinically in use. Here we introduce that operational tolerance, based on hypertrophy to hyperplasia switch upon liver regeneration, is early achieved and maintained well in half-size liver allograft transplantation through host bone marrow stem cells repopulation and 9-day immunosuppression. Compared with whole and partial rat liver transplantations as the controls, longer-term survivals (over 430 days) were observed in the tolerant hosts (p= 0.001), the allografts functioned well and no acute or chronic rejections were confirmed by histology examinations. Further study revealed that the allograft was reinstituted by host-derived stem cells marked with CD34, which migrated, repopulated and differentiated after mobilization. However donor-specific hyporesponse was not achieved through skin transplantation, indicating no adaptive immune activity occurrence. Our protocol is characteristic of targeting the allografts and almost no immunological intervention, offering a novel avenue to operational tolerance induction which is of highly clinical relevance.

immunology↗

bioRxiv2022

High throughput RNA sequencing discovers symptomatic and latent viruses: an example from ornamental Hibiscus

Hibiscus rosa-sinensis L. (Hibiscus, Malvaceae) is an ornamental species grown widely in amenity plantings. We collected leaves on an urban roadside pavement (sidewalk) near a market in Guangzhou which showed multiple symptoms of leaf rolling, deformation and chlorosis. Initial evaluation by electron microscopy using negative staining of drip preparations revealed the presence of tobamovirus-like particles. Total RNA was extracted, and, unusually, without any RNA selection based on sequence, was used for cDNA library construction and high-throughput survey sequencing. From the 814 Mb of clean sequence data (from 2,712,161 paired reads of 150 bp) reads representing chloroplast, ribosomal, and mitochondrial genes were filtered out, eliminating 79.1% of reads. 1,135,848 x 150 bp of the sequence was retained and screened for viral sequences. Assembly of these sequences detected nine virus species from seven virus genera comprising three tobamoviruses, namely, Tobacco mosaic virus, Tobacco mild green mosaic virus and Hibiscus latent Singapore virus, Turnip mosaic virus (Potyvirus), Potato virus M (Carlavirus), Hibiscus chlorotic ringspot virus (Betacarmovirus), Fabavirus sp (Fabavirus), Cotton leaf curl Multan virus (Begomovirus) and a putative mitoviruses replicating in mitochondria, Chenopodium quinoa mitovirus 1. Mapping the reads to complete virus reference sequences showed high and uniform coverage of the genomes from 3,729 x coverage for Turnip mosaic virus to 22 x for Cotton leaf curl Multan virus. By comparison, nuclear reference genes actin showed 14 x coverage and polyubiquitin 27 x. Notable variants from reference sequences (SNPs) were identified. With the low cost of sequencing and potential for semi-automated bioinformatic pipelines, the whole-RNA approach has huge potential for identifying multiple undiagnosed viruses in ornamental plants, resulting in the ability to take preventive measures in production facilities against spread and to product quality for the mutual benefit of producers and consumers.

genomics↗

bioRxiv2022

Identification of Piperlongumine (PL) as an new E3 ligase ligand to induce targeted protein degradation

PROteolysis Targeting Chimeras (PROTACs) are bifunctional molecules that degrade target proteins through recruiting E3 ligases. However, their application is limited in part because few E3 ligases can be recruited by known E3 ligase ligands. In this study, we identified piperlongumine (PL), a natural product, as a covalent E3 ligase recruiter, which induces CDK9 degradation when it is conjugated with SNS-032, a CDK9 inhibitor. The lead conjugate 955 can potently degrade CDK9 in a ubiquitin-proteasome-dependent manner and is much more potent than SNS-032 against various tumor cells in vitro. Mechanistically, we identified KEAP1 as the E3 ligase recruited by 955 to degrade CDK9 through a TurboID-based proteomics study, which was further confirmed by KEAP1 knockout and the nanoBRET ternary complex formation assay. In addition, PL-Ceritinib conjugate can degrade EML4-ALK fusion oncoprotein, suggesting that PL may have a broader application as a covalent E3 ligase ligand in targeted protein degradation.

cancer biology↗

bioRxiv2022

Core Transcription Programs Controlling Injury-Induced Neurodegeneration of Retinal Ganglion Cells

Neurodegenerative diseases are characterized by neuronal death and regenerative failure. However, gene regulatory programs governing how initial neuronal injuries lead to neuronal death remain poorly understood. In adult mice, optic nerve crush (ONC) injury, which severs all axons of retinal ganglion cells (RGCs), results in massive death of axotomized RGCs and regenerative failure of survivors. We performed an in vivo CRISPR/Cas9-based genome-wide screen of 1893 transcription factors (TFs) to seek repressors of RGC survival and axon regeneration following ONC. In parallel, we profiled the epigenetic and transcriptional landscapes of injured RGCs by ATAC-seq and RNA-seq to identify critical injury responsive TFs and their targets. Remarkably, these independent analyses converged on a set of four ATF/CEBP transcription factors - ATF3, ATF4, C/EBP{gamma} and CHOP (Ddit3) - as critical regulators of survival. Further studies indicate that these TFs contribute to two pro-death transcriptional programs: ATF3/CHOP preferentially regulate pathways activated by cytokines and innate immunity, whereas ATF4/C/EBP{gamma} regulate pathways engaged by intrinsic neuronal stressors. Manipulation of these TFs also protects RGCs in an experimental model of glaucoma, a prevalent disease in which RGCs die. Together, our results reveal core transcription programs that transform an initial axonal insult into a degenerative result and suggest novel strategies for treating neurodegenerative diseases.

neuroscience↗

bioRxiv2022

Evaluation of the anti-tumor activities of Sulfonylurea Derivatives

This study prepared 25 sulfonylurea compounds to evaluate anti-tumor activity. Through experimental investigations in MDA-MB-231 and MCF-7, i.e., cell lines of breast carcinoma of human, we have concluded that some compounds can significantly suppress breast carcinoma cells from growing and proliferating. Moreover, the compound Ms inhibitory effect on cells of breast carcinoma is concentration-dependent under a certain treatment time; and the inhibitory effect of the compound M on breast carcinoma cells is time-dependent under a certain concentration. In addition, we also found that the compound M can effectively suppress cells of breast carcinoma from migration and independent survival. The results can show the prospect of research and development of new breast carcinoma treatment drug.

biochemistry↗

bioRxiv2021

Emerging SARS-CoV-2 Variants of Concern: Spike Protein Mutational Analysis and Epitope for Broad Neutralization

Mutations in the spike glycoproteins of SARS-CoV-2 variants of concern have independently been shown to enhance aspects of spike protein fitness. Here, we report the discovery of a novel antibody fragment (VH ab6) that neutralizes all major variants, with a unique mode of binding revealed by cryo-EM studies. Further, we provide a comparative analysis of the mutational effects within variant spikes and identify the structural role of mutations within the NTD and RBD in evading antibody neutralization. Our analysis shows that the highly mutated Gamma N-terminal domain exhibits considerable structural rearrangements, partially explaining its decreased neutralization by convalescent sera. Our results provide mechanistic insights into the structural, functional, and antigenic consequences of SARS-CoV-2 spike mutations and highlight a spike protein vulnerability that may be exploited to achieve broad protection against circulating variants.

biochemistry↗