Advances in CRISPR-Cas systems for RNA targeting, tracking and editing

Wang, Fei,Wang, Lianrong,Zou, Xuan,Duan, Suling,Li, Zhiqiang,Deng, Zixin,Luo, Jie,Lee, Sang Yup,Chen, Shi Elsevier 2019 BIOTECHNOLOGY ADVANCES Vol.37 No.5

<P><B>Abstract</B></P> <P>Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) systems, especially type II (Cas9) systems, have been widely used in gene/genome targeting. Modifications of Cas9 enable these systems to become platforms for precise DNA manipulations. However, the utilization of CRISPR-Cas systems in RNA targeting remains preliminary. The discovery of type VI CRISPR-Cas systems (Cas13) shed light on RNA-guided RNA targeting. Cas13d, the smallest Cas13 protein, with a length of only ~930 amino acids, is a promising platform for RNA targeting compatible with viral delivery systems. Much effort has also been made to develop Cas9, Cas13a and Cas13b applications for RNA-guided RNA targeting. The discovery of new RNA-targeting CRISPR-Cas systems as well as the development of RNA-targeting platforms with Cas9 and Cas13 will promote RNA-targeting technology substantially. Here, we review new advances in RNA-targeting CRISPR-Cas systems as well as advances in applications of these systems in RNA targeting, tracking and editing. We also compare these Cas protein-based technologies with traditional technologies for RNA targeting, tracking and editing. Finally, we discuss remaining questions and prospects for the future.</P> <P><B>Highlights</B></P> <P> <UL> <LI> RNA targeting and editing are becoming increasingly important </LI> <LI> CRISPR-Cas systems are advancing for RNA targeting, tracking and editing </LI> <LI> The type VI CRISPR-Cas systems are useful for RNA-guided RNA targeting </LI> <LI> Use of Cas9 and Cas13 will advance RNA-targeting technologies </LI> </UL> </P>

Effect of the Ag-doping on the phase structural evolution, dielectric and ferroelectric properties of lead-free niobate ceramics

Huining Wang,Zixin Zhang,QuanSen Yang,Fangfang Wang,Kang Yan 대한금속·재료학회 2022 ELECTRONIC MATERIALS LETTERS Vol.18 No.2

Ionic doping is an important approach to modification of crystal structure and physical properties of the piezoelectric ceramics. In this work, the lead-free piezoelectric ceramic (1- x )K 0.18 Na 0.74 Li 0.08 NbO 3 - x AgNbO 3 (abbreviated as KNLN- x AN, 0 ≤ x ≤ 0.8) was prepared by conventional solid-state reaction method. The effect of the Ag doping on the phase structure, dielectric and ferroelectric properties of the KNLN-based ceramics was investigated by the XRD, DSC, dielectric and ferroelectric characterizations. It is found that all KNLN- x AN ceramics show single phase in perovskite structure because the ionic radii of dopant Ag close to the average ionic size at the A-site in KNLN. The KNLN- x AN exhibits the rhombohedral to orthorhombic phase transition at room temperature and the Curie temperature ( T C ) decreases to low temperature with increasing x value. A narrow tetragonal phase region and a wide orthorhombic phase region form for the compositions with x ≥ 0.4, indicating that the Ag doping stabilizes orthorhombic phase in wide temperature for the KNLN. A ferroelectric anomalies due to high electrical field induced phase transition is found in the sample with x = 0.1. When x = 0.4, high Curie temperature ( T C = 380 °C), large remnant polarization ( P r = 24.4 μC/cm 2 ) and high dielectric constant ( ε r = 10,000 at 1 kHz) at T C are achieved.

Virtual Model Reduction-based Control Strategy of Planar Three-link Underactuated Manipulator with Middle Passive Joint

Zixin Huang,Xuzhi Lai,Pan Zhang,Yawu Wang,Min Wu 제어·로봇·시스템학회 2021 International Journal of Control, Automation, and Vol.19 No.1

This paper presents a position control strategy for a planar active-passive-active (APA) underactuatedmanipulator with second-order nonholonomic characteristics. According to the structural characteristics of the planar APA system, we divide the system into two parts: a planar virtual Pendubot (PVP) and a planar virtual Acrobot(PVA). For the PVP, we mainly fulfill the target angle of the first link, which is calculated through the geometrymethod, and make the system stable. In this stage, via keeping the states of the third link being zero, the system isreduced to the PVP. Meanwhile, we design an open-loop control law based on the nilpotent approximation (NA)model of the PVP to make the second link stable and the first link stabilize at its target angle. Then, the planar APAsystem is reduced to a PVA with all links’ angular velocities being zero. For the PVA, we mainly realize the othertwo links’ target angles obtained via the particle swarm optimization (PSO) algorithm. Thus, the control objectiveof the planar APA system is achieved. Finally, above control strategy is verified by simulation results.

Pectin oligosaccharides improved lipid metabolism in white adipose tissue of high-fat diet fed mice

Zixin Fan,Xuejiao Chen,Tianzhi Liu,Qianhui Yu,Ziqi Song,Fei Wang,Tuoping Li 한국식품과학회 2022 Food Science and Biotechnology Vol.31 No.9

Impacts of pectin oligosaccharide (POS) got from hawthorn fruitage on adiponectin signaling pathway and white adipose metabolism in mice fed with high-fat control. The results showed that POS significantly inhibited the levels of inflammatory cytokines TNF-α and IL-6, and down-regulated expression of CD68. POS dramatically reduced gene expression contents of fatty acid composite concerning enzymes ACC and FAS, as well as TG synthesis-related enzymes SCD-1 and DGAT1 as compared to a high-fat group (HFC). POS dramatically increased expression levels of oxidation-related enzymes of fatty acid ACO, CPT-1, and TG deposition-related enzymes ATGL and HSL as contrast to the high-fat control group. In addition, POS activated adiponectin-mediated AdipoR1/AMPK/PPARα signaling path by upregulating expression levels of AdipoR1, AMPK and PPARα. The results demonstrated that POS can improve lipid metabolism of adipose tissue, and contribute to the creation of functional foods to prevent and treat lipid metabolism disorders.

Relay selection and Optimization algorithm of Power allocation based on Channel Delay for UWSN

YunLi,Zhigang Jin,Xunjun Wang,Zixin Liu 보안공학연구지원센터 2016 International Journal of Future Generation Communi Vol.9 No.2

In the light of the characteristics of random change that underwater sensor change by time, space and frequency, select the best relay node to improve communication quality and get the diversity gain. A new optimal relay selection method is proposed in this paper, by considering two indexes synthetically that channel gain and underwater acoustic communication long time delay to select the best relay node. Based on the best relay node and minimization of bit error rate to take optimal power allocation of source node and relay node to realize network error rate’s reduction of 1.81 dB so then improve the overall performance of the network.

Occurrence, evolution, and functions of DNA phosphorothioate epigenetics in bacteria

Tong, Tong,Chen, Si,Wang, Lianrong,Tang, You,Ryu, Jae Yong,Jiang, Susu,Wu, Xiaolin,Chen, Chao,Luo, Jie,Deng, Zixin,Li, Zhiqiang,Lee, Sang Yup,Chen, Shi National Academy of Sciences 2018 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.115 No.13

<P><B>Significance</B></P><P>Phosphorothioate (PT) modification of the DNA sugar-phosphate backbone is an important microbial epigenetic modification governed by DndABCDE, which together with DndFGH, constitutes a restriction-modification system. We show that up to 45% of 1,349 identified bacterial <I>dnd</I> systems exhibit the form of solitary <I>dndABCDE</I> without the restriction counterparts of <I>dndFGH</I>. The combination of epigenomics, transcriptome analysis, and metabolomics suggests that in addition to providing a genetic barrier against invasive DNA, PT modification is a versatile player involved in the epigenetic control of gene expression and the maintenance of cellular redox homeostasis. This finding provides evolutionary and functional insights into this unusual epigenetic modification. Our results imply that PT systems might evolve similar to other epigenetic modification systems with multiple cellular functions.</P><P>The chemical diversity of physiological DNA modifications has expanded with the identification of phosphorothioate (PT) modification in which the nonbridging oxygen in the sugar-phosphate backbone of DNA is replaced by sulfur. Together with DndFGH as cognate restriction enzymes, DNA PT modification, which is catalyzed by the DndABCDE proteins, functions as a bacterial restriction-modification (R-M) system that protects cells against invading foreign DNA. However, the occurrence of <I>dnd</I> systems across a large number of bacterial genomes and their functions other than R-M are poorly understood. Here, a genomic survey revealed the prevalence of bacterial <I>dnd</I> systems: 1,349 bacterial <I>dnd</I> systems were observed to occur sporadically across diverse phylogenetic groups, and nearly half of these occur in the form of a solitary <I>dndBCDE</I> gene cluster that lacks the <I>dndFGH</I> restriction counterparts. A phylogenetic analysis of 734 complete PT R-M pairs revealed the coevolution of M and R components, despite the observation that several PT R-M pairs appeared to be assembled from M and R parts acquired from distantly related organisms. Concurrent epigenomic analysis, transcriptome analysis, and metabolome characterization showed that a solitary PT modification contributed to the overall cellular redox state, the loss of which perturbed the cellular redox balance and induced <I>Pseudomonas fluorescens</I> to reconfigure its metabolism to fend off oxidative stress. An in vitro transcriptional assay revealed altered transcriptional efficiency in the presence of PT DNA modification, implicating its function in epigenetic regulation. These data suggest the versatility of PT in addition to its involvement in R-M protection.</P>

Study on the damping mechanisms of a suspended particle damper attached to a wind turbine tower

Chenzhi Ma,Zheng Lu,Dianchao Wang,Zixin Wang 한국풍공학회 2021 Wind and Structures, An International Journal (WAS Vol.33 No.1

Intensive attention has been given to mitigating the dynamic responses of wind turbine towers (WTs) under wind and seismic excitations to ensure their safety and serviceability. This study details the damping mechanisms of a suspended particle damper (suspended PD) on the vibration control of a horizontal-axis WT. This damper combines the benefits of a tuned mass damper (TMD) and fixed PD, and can be effective without an external damping system. It therefore is a more practical solution for the vibration control of a WT. In this study, a finite element WT is built, and two damper systems with a TMD and suspended PD are modeled and compared. Ground motions and strong lateral winds are applied as external excitations to the operational and parked turbines, respectively. A full factorial study using a statistical method is conducted to determine the interaction effects of key parameters of the suspended PD. Results show that the damping effectiveness of a suspended PD is not sensitive to the external damping system under specific parameters, and it can be effective in detuned cases. Finally, a comparison between the optimal TMD and suspended PD on the vibration control of a WT is performed. The comparative results indicate that the performance of the suspended PD is considerably more robust than the TMD in wind-seismic excitations.

Hyperbaric Oxygen Pretreatment Improves Cognition and Reduces Hippocampal Damage Via p38 Mitogen-Activated Protein Kinase in a Rat Model

Baisong Zhao,Xingrong Song,Yongying Pan,Zixin Wang,Haiping Xu 연세대학교의과대학 2017 Yonsei medical journal Vol.58 No.1

Purpose: To investigate the effects of hyperbaric oxygen (HBO) pretreatment on cognitive decline and neuronal damage in an Alzheimer’sdisease (AD) rat model. Materials and Methods: Rats were divided into three groups: normal saline (NS), AD, and HBO+AD. In the AD group, amyloid β peptide (Aβ)1-40 was injected into the hippocampal CA1 region of the brain. NS rats received NS injection. In the HBO+AD group, rats received 5 days of daily HBO therapy following Aβ1-40 injection. Learning and memory capabilities were examined using the Morris water maze task. Neuronal damage and astrocyte activation were evaluated by hematoxylin-eosin staining and immunohistochemistry,respectively. Dendritic spine density was determined by Golgi-Cox staining. Tumor necrosis factor-α, interleukin-1β, and interleukin-10 production was assessed by enzyme-linked immunosorbent assay. Neuron apoptosis was evaluated by terminal deoxynucleotidyl transferase dUTP nick end labeling. Protein expression was examined by western blotting. Results: Learning and memory dysfunction was ameliorated in the HBO+AD group, as shown by significantly lower swimming distances and escape latency, compared to the AD group. Lower rates of neuronal damage, astrocyte activation, dendritic spine loss, and hippocampal neuron apoptosis were seen in the HBO+AD than in the AD group. A lower rate of hippocampal p38 mitogen-activated protein kinase (MAPK) phosphorylation was observed in the HBO+AD than in the AD group. Conclusion: HBO pretreatment improves cognition and reduces hippocampal damage via p38 MAPK in AD rats.

Sliding Mode Predictive Active Fault-tolerant Control Method for Discrete Multi-faults System

Pu Yang,Zhangxi Liu,Dejie Li,Zhiqing Zhang,Zixin Wang 제어·로봇·시스템학회 2021 International Journal of Control, Automation, and Vol.19 No.3

For discrete systems with sensor and actuator failures, this paper proposes an observer that can estimate both sensor failures and actuator failures and designs a sliding mode predictive fault-tolerant control method based on an improved whale optimization algorithm. First, a proportional-integral observer that can observe actuator fault and sensor fault is designed to estimate the value of faults, which greatly improves the work efficiency. After that, a global sliding mode surface is designed as a prediction model, so that the initial state of the system is located on the sliding mode surface to avoid the instability of the sliding mode approaching the process. The reference trajectory of a power function with uncertainty and disturbance compensation is designed to reduce the bad influence of uncertainty and disturbance on the system and suppress chattering greatly. Meanwhile, in the rolling optimization part, an improved whale optimization algorithm(IWOA) is designed to optimize the control law. Finally, the simulation results on the four-rotor helicopter simulation platform show the practicability and superiority of the algorithm.

A three-dimensional two-hemisphere model for unmanned aerial vehicle multiple-input multiple-output channels

Zixu Su,Wei Chen,Changzhen Li,Junyi Yu,Guojiao Gong,Zixin Wang 한국전자통신연구원 2023 ETRI Journal Vol.45 No.5

The application of unmanned aerial vehicles (UAVs) has recently attracted considerable interest in various areas. A three-dimensional multiple-input multiple-output concentric two-hemisphere model is proposed to characterize the scattering environment around a vehicle in an urban UAV-to-vehicle communication scenario. Multipath components of the model consisted of lineof-sight and single-bounced components. This study focused on the key parameters that determine the scatterer distribution. A time-variant process was used to analyze the nonstationarity of the proposed model. Vital statistical properties, such as the space–time–frequency correlation function, Doppler power spectral density, level-crossing rate, average fade duration, and channel capacity, were derived and analyzed. The results indicated that with an increase in the maximum scatter radius, the time correlation and levelcrossing rate decreased, the frequency correlation function had a faster downward trend, and average fade duration increased. In addition, with the increase of concentration parameter, the time correlation, space correlation, and levelcrossing rate increased, average fade duration decreased, and Doppler power spectral density became flatter. The proposed model was compared with current geometry-based stochastic models (GBSMs) and showed good consistency. In addition, we verified the nonstationarity in the temporal and spatial domains of the proposed model. These conclusions can be used as references in the design of more reasonable communication systems.