Biology subjects

Gong, P.

Publications and source records attributed to Gong, P..

24 records · Page 2Linked to original sources

bioRxiv2021

Geminiviral genomes encode additional proteins with specific subcellular localizations and virulence function

Geminiviruses are plant viruses with limited coding capacity. Geminivirus-encoded proteins were identified applying a 10-kDa arbitrary threshold; however, it is increasingly clear that small proteins play relevant roles in biological systems, which calls for the reconsideration of this criterion. Here, we show that geminiviral genomes contain additional ORFs. Using tomato yellow leaf curl virus, we demonstrate that some of these novel ORFs are expressed during the infection, and that the encoded proteins display specific subcellular localizations. We prove that the largest of these new ORFs, which we name V3, is required for full viral infection, and that the V3 protein localizes in the Golgi apparatus and functions as an RNA silencing suppressor. These results imply that the repertoire of geminiviral proteins can be expanded, and that getting a comprehensive overview of the molecular plant-geminivirus interactions will require the detailed study of small ORFs so far neglected.

plant biology↗

bioRxiv2020

Fractional diffusion theory of balanced heterogeneous neural networks

Interactions of large numbers of spiking neurons give rise to complex neural dynamics with fluctuations occurring at multiple scales. Understanding the dynamical mechanisms underlying such complex neural dynamics is a long-standing topic of interest in neuroscience, statistical physics and nonlinear dynamics. Conventionally, fluctuating neural dynamics are formulated as balanced, uncorrelated excitatory and inhibitory inputs with Gaussian properties. However, heterogeneous, non-Gaussian properties have been widely observed in both neural connections and neural dynamics. Here, based on balanced neural networks with heterogeneous, non-Gaussian features, our analysis reveals that in the limit of large network size, synaptic inputs possess power-law fluctuations, leading to a remarkable relation of complex neural dynamics to the fractional diffusion formalisms of non-equilibrium physical systems. By uniquely accounting for the leapovers caused by the fluctuations of spiking activity, we further develop a fractional Fokker-Planck equation with absorbing boundary conditions. This body of formalisms represents a novel fractional diffusion theory of heterogeneous neural networks and results in an exact description of the network activity states. This theory is further implemented in a biologically plausible, balanced neural network and identifies a novel type of network state with rich, nonlinear response properties, providing a unified account of a variety of experimental findings on neural dynamics at the individual neuron and the network levels, including fluctuations of membrane potentials and population firing rates. We illustrate that this novel state endows neural networks with a fundamental computational advantage; that is, the neural response is maximised as a function of structural connectivity. Our theory and its network implementations provide a framework for investigating complex neural dynamics emerging from large networks of spiking neurons and their functional roles in neural processing.

neuroscience↗

bioRxiv2020

sgRNA level determines CRISPRi knockdown efficiency in K562 cells

To determine how nuclease deactivated Cas9 (dCas9) or sgRNA expression level affects the knockdown efficiency of CRISPRi, K562 cell clones expressing KRAB-dCas9 protein either with the inducible Tet-on system or with the constitutive SFFV promotor were created by lentiviral transduction, and single clones were selected by fluorescence-activated cell sorting (FACS) for further study. Six genes with various expression levels were targeted using lentiviral sgRNA from two libraries in four cell clones with various KRAB-dCas9 expression levels. We determined the knockdown efficiency and the expression level of the dCas9 protein /sgRNA level by flow cytometry. The cell clone with the highest KRAB-dCas9 expression level achieved effective CRISPRi knockdown, and is statistically different from other clones, indicating enough KRAB-dCas9 expression might be a prerequisite for CRISPRi. Utilizing this clone, we modified the expression level of sgRNA by adopting different multiplicity of infection (MOI)in lentiviral transduction and found that the knockdown efficiency was neither affected by the target gene expression level nor does it correlate with KRAB-dCas9 level, which remained relatively constant (CV=2.2%) across knockdown experiments. 74.72%, 72.28%, 39.08% knockdown of mmadhc, rpia, znf148 genes were achieved, and the knockdown efficiency correlated well with the sgRNA expression level. Linear regression modeling of the data revealed that the knockdown efficiency is significantly affected by both KRAB-dCas9 and sgRNA level, and the sgRNA level has a greater impact, based on the standardized coefficient (0.525 for KRAB-dCas9, 0.981 for sgRNA), indicating that sgRNA level is a major factor affecting CRISPRi efficiency.

cancer biology↗

bioRxiv2020

Targeting Aryl Hydrocarbon Receptor with small molecule, 1'H-indole-3'-carbonyl -thiazole-4-carboxylic acid methyl ester blocked human glioma cell invasion via MYH9

Aryl hydrocarbon receptor (AHR) was a master regulator of anti-tumor cell migration in various cell types. Whether and how AHR regulates glioma cell migration is largely unknown. We found that small molecule 2-(1'H-indole-3'-carbonyl)-thiazole-4-carboxylic acid methyl ester (ITE), an endogenous AHR ligand, can significantly block glioma cell migration and invasion in vitro, ex vivo and in vivo. Knocking down AHR by siRNA abolished ITEs migration-inhibiting effects. ITE increased the number of filopodia-like protrusion formation, but reduced protrusion attachment to the extracellular matrix, and inhibited the rear retraction of migrating glioma cells. Moreover, both mesenchymal and amoeboid migrating cells were observed in the DMSO control group while none of the cells display amoeboid migration in the ITE treated group. MYH9 was significantly reduced by ITE treatment in human glioma cells. Over-expression of MYH9 abrogated ITEs migration-inhibiting effects, with the expression level of MYH9 correlated with cell migration ability. Since MYH9 is a component of non-muscle myosin IIA (NMIIA), which is essential for cell migration in 3D confined space, and not a discovered target of AHR, the fact that ITE affects MYH9 via AHR opens a new research and development avenue.

cell biology↗

bioRxiv2019

Semaphorin 3a reduces the side effects of radiation on BMSCs by reducing ROS

1.Background/AimsRadiotherapy does not only kill tumor cells but also impairs the function of adjacent tissues, especially bone metabolism by damaging bone marrow stromal stem cells (BMSCs). This study aimed to investigate the effect of semaphorin 3a (Sema3a) on BMSCs exposed to 2 Gy radiation. MaterialsBMSCs were divided into four groups, namely, group A (0 Gy), group B (2 Gy), group C (0 Gy + Sema3a), and group D (2 Gy + Sema3a). A Cell Counting Kit-8 kit, Alizarin-Red and Oil-Red-O staining, alkaline phosphatase activity kit, and dichlorodihydro-fluoresce in diacetate were used to test cell proliferation, cell cycle, osteogenic ability, adipogenic ability, and the level of reactive oxygen species (ROS), respectively, in each group. Real-time PCR was performed to test the expression of osteogenic (osteocalcin and Runt-related transcription factor 2), adipogenic (peroxisome proliferator-activated receptor gamma), interleukin (IL)-6, and tumor necrosis factor (TNF)- genes. ResultsBMSC proliferation, osteogenic differentiation, and the number of cells undergoing division (S+G2 phase of the cell cycle) were found to be lower in group B than in group A. and the cellular levels of ROS, adipogenic differentiation, and expression of inflammatory factors (IL-6 and TNF-) were higher in group B than in group A. Furthermore, osteogenic differentiation ability was higher in group D than in group B, and adipogenic differentiation ability, cellular levels of ROS, and gene expression of TNF- and IL-6 were lower in group D than in group B. ConclusionThis study demonstrated that 2 Gy radiation could decrease the osteogenic differentiation ability of BMSCs and increase their adipogenic differentiation ability by increasing the production of ROS. However, Sema3a could reduce these side effects by decreasing the levels of ROS.

cell biology↗

bioRxiv2019

Changes in spinal cord hemodynamic reflect modulation of spinal network with different parameters of epidural stimulation

In this study functional ultrasound (fUS) imaging has been implemented to explore the local hemodynamic response induced by electrical epidural stimulation and to study real-time in vivo functional changes of the spinal cord, taking advantage of the superior spatiotemporal resolution provided by fUS. By quantifying the hemodynamic and electromyographic response features, we tested the hypothesis that the transient hemodynamic response of the spinal cord to electrical epidural stimulation could reflect modulation of the spinal circuitry and accordingly respond to the changes in parameters of electrical stimulation. The results of this study for the first time demonstrate that the hemodynamic response to electrical stimulation could reflect functional organization of the spinal cord. Response in the dorsal areas to epidural stimulation was significantly higher and faster compared to the response in ventral spinal cord. Positive relation between the hemodynamic and the EMG responses was observed at the lower frequencies of epidural stimulation (20 and 40 Hz), which according to our previous findings can facilitate spinal circuitry after spinal cord injury, compared to higher frequencies (200 and 500 Hz). These findings suggest that different mechanisms could be involved in spinal cord hemodynamic changes during different parameters of electrical stimulation and for the first time provide the evidence that functional organization of the spinal cord circuitry could be related to specific organization of spinal cord vasculature and hemodynamic.\n\nSignificance StatementElectrical epidural stimulation (EES) has been successfully applied to control chronic refractory pain and was evolved to alleviate motor impairment after spinal cord injury, in Parkinsons disease, and other neurological conditions. The mechanisms underlying the EES remain unclear, and current methods for monitoring EES are limited in sensitivity and spatiotemporal resolutions to evaluate functional changes in response to EES. We tested the hypothesis that the transient hemodynamic response of the spinal cord to EES could reflect modulation of the spinal cord circuitry and accordingly respond to the changes in parameters of EES. The proposed methodology opens a new direction for quantitative evaluation of the spinal cord hemodynamic in understanding the mechanisms of spinal cord functional organization and effect of neuromodulation.

neuroscience↗