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>

Knowledge Acquisition Approach Based on Rough Set in Online Aided Decision System for Food Processing Quality and Safety

Liu Peng,Liu Wen,Li Qiang,Yang Li,Duan Min,Dai Yue 보안공학연구지원센터 2014 International Journal of u- and e- Service, Scienc Vol.7 No.6

For the problem that the use effect of food processing information system is poor due to absence of knowledge acquisition measures and knowledge self-updating function, a knowledge acquisition approach based on rough set is put forward. First, the approach establishes a set of predicted samples for the relationship between food processing parameters and product quality; then uses the discretization of continuous attribute, attribute reduction and rule extraction algorithm of rough set to acquire automatically predicted knowledge from a large number of predicted sample sets, and then saves the predicted knowledge in the knowledge base of expert system; finally, realizes the extraction of knowledge of food processing process based on the inference engine, which greatly enhances the effectiveness and practicality of the acquired knowledge in online aided decision system of the food processing quality and safety.

Quantitative Susceptibility Mapping of Brain Iron Deposition in Patients With Recurrent Depression

Duan Xinxiu,Xie Yuhang,Zhu Xiufang,Chen Lei,Li Feng,Feng Guoquan,Li Lei 대한신경정신의학회 2022 PSYCHIATRY INVESTIGATION Vol.19 No.8

Objective Recurrence is the most significant feature of depression and the relationship between iron and recurrent depression is still lack of direct evidence in vivo.Methods Twenty-one patients with depression and twenty control subjects were included. Gradient-recalled echo, T1 and T2 images were acquired using a 3.0T MRI system. After quantitative susceptibility mapping were reconstructed and standardized, a whole-brain and the regions of interest were respectively analyzed.Results Significant increases in susceptibility were found in multiple recurrent depression patients, which involved several brain regions (frontal lobes, temporal lobe structures, occipital lobes hippocampal regions, putamen, thalamus, cingulum, and cerebellum). Interestingly, no susceptibility changes after treatment compared to pre-treatment (all p>0.05) and no significant correlation between susceptibility and Hamilton Depression Rating Scale were found. Besides, it was close to significance that those with a higher relapse frequency or a longer mean duration of single episode had a higher susceptibility in the putamen, thalamus, and hippocampus. Further studies showed susceptibility across the putamen (ρ²=0.27, p<0.001), thalamus (ρ²=0.21, p<0.001), and hippocampus (ρ²=0.19, p<0.001) were strongly correlated with total course of disease onset.Conclusion Brain iron deposition is related to the total course of disease onset, but not the severity of depression, which suggest that brain iron deposition may be a sign of brain damage in multiple recurrent depression.

Commutation Compensation Strategy for Brushless DC Motor Based on Terminal Voltage Reconstruction

Li Guidan,Zhang Tianqi,Li Bin,Fu Tongling,Duan Peihua 대한전기학회 2021 Journal of Electrical Engineering & Technology Vol.16 No.4

In the sensorless brushless DC (BLDC) motor control system, the commutation signal is the key to measure the system performance. To improve the commutation accuracy, a commutation compensation strategy based on terminal voltage reconstruction is proposed. By analyzing the commutation process, the integral of ideal terminal voltage is adopted to determine the commutation error. Then considering the voltage clamping of the freewheel diode, the actual terminal voltage is analyzed in diff erent periods. In the non-commutation period, a PWM cycle is divided into three regions, and the corresponding duration can be calculated by fl oating phase current, and then the equality of actual and ideal terminal voltage integrals is revealed. In the commutation period, the instantaneous value of back-electromotive force (back-EMF) at commutation point is used to construct the ideal terminal voltage and the commutation time is determined by the edge detection. In this way, the integral of terminal voltage can be calculated precisely. Then the error index is introduced and the relationship between the commutation error and the error index is presented. To eliminate the commutation error, the PI controller is adopted which outputs the compensation angle. The proposed strategy avoids the phase shift errors and the accumulation of integral errors, moreover the feasibility and eff ectiveness are verifi ed by simulations and experiments under diff erent conditions. In addition, the strategy can also be used to correct the installation error of Hall sensor

Synthesis of Poly(L,L-lactic acid-co-lysine) and Its Cell Compatibility Evaluation as Coating Material on Metal

Li Jie Duan,김민지,정직한,정동준,김지흥 한국고분자학회 2010 Macromolecular Research Vol.18 No.8

This study evaluated and compared the cell adhesion and spreading behavior on the surfaces of biodegradable poly(L,L-lactic acid) (PLA) and poly(L,L-lactic acid-co-lysine) (PLAL) films. The thermal stability and film surface properties were examined by differential scanning calorimetry (DSC), thermal gravimetric analysis (TGA), contact angle, and scanning electron microscopy (SEM) to assess the physicochemical characteristics affecting the cell adhesion behavior of materials, PLA and PLAL. Mouse fibroblast cells were cultured on the surface of stainless steel wafers coated with PLA and PLAL. SEM images showed most of the cells spreading slightly on the PLA coating film with a linkage of cellular pseudopods. The degree of cell spreading on the PLAL surface would be higher than that of PLA due to the side-chain effect of (+) charged amino groups easily inducing cell adhesion and spreading. Moreover, the cell viability was also evaluated on PLA and PLAL using a MTT assay, and no acute cytotoxicity was observed.

Interference of periostin attenuates pathological changes, proinflammatory markers and renal fibrosis in diabetic kidney injury

Duan Xiaoting,Chen Cheng,Liu Xiaoli,Wang Taoxia,Feng Shuning,Li Jianwei,Li Guiying 한국유전학회 2023 Genes & Genomics Vol.45 No.11

Background Diabetic nephropathy (DN) is a prevalent complication of diabetes, in which inflammation and fibrosis are the significant pathogenesis. Periostin is a matricellular protein that functions on stabilizing the extracellular matrix by binding to integrins during development. This study aimed to explored the role of periostin in DN. Methods The animal and cell models of DN were constructed in streptozocin (STZ)-induced mice and high glucose-challenged human mesangial cells (HMCs). The role of periostin in pathological changes, inflammation and fibrosis in DN was investigated through biochemical detection, HE and Masson staining and scores, western blot, enzyme‑linked immunosorbent assay (ELISA) and real-time quantitative PCR (RT-qPCR) assays. Results Knockdown of periostin counteracted the STZ-induced the ratio of kidney weight and body weight, and the concentrations of urine albumin excretion (UAE), serum creatinine (Scr), urine albumin/creatinine ratio (UACR) and blood urea nitrogen (BUN) in mice. Moreover, silencing of periostin alleviated the pathological manifestations and reduced the concentrations of IL-6, TNF-α and IL-1β in mice kidney tissues and sera. Also, downregulation of periostin decreased the relative protein expression of fibronectin, collagen IV and α-SMA in kidney tissues. Meanwhile, interference of periostin attenuated the levels of pro-inflammation factors and the expressions of fibrosis markers in HG-induced HMCs. Conclusion Interference of periostin resisted DN via attenuating the pro-inflammatory cytokines release and renal fibrosis in diabetic kidney injury. Our study establishes a basis for its further study and underlying application in clinical practice in diagnosing and treating diabetic kidney injury or other relevant diseases.

Correlation analysis of the wind of a cable-stayed bridge based on field monitoring

Li, Hui,Laima, Shujin,Li, Na,Ou, Jinping,Duan, Zhondong Techno-Press 2010 Wind and Structures, An International Journal (WAS Vol.13 No.6

This paper investigates the correlation of wind characteristics monitored on a cable-stayed bridge. Total five anemoscopes are implemented into the bridge. Two out of 5 anemoscopes in inflow and two out of 5 anemoscopes in wake-flow along the longitudinal direction of the bridge are installed. Four anemoscopes are respectively distributed at two cross-sections. Another anemoscope is installed at the top of the tower. The correlation of mean wind speed and direction, power spectral density, the turbulent intensity and integral length of wind in flow at two cross-sections are investigated. In addition, considering the non-stationary characteristics of wind, the spatial correlation in time-frequency is analyzed using wavelet transform and different phenomenon from those obtained through FFT is observed. The time-frequency analysis further indicates that intermittence, coherence structures and self-similar structures are distinctly observed from fluctuant wind. The flow characteristics around the bridge deck at two positions are also investigated using the field measurement. The results indicate that the mean wind speed decrease when the flow passing through the deck, but the turbulence intensity become much larger and the turbulence integral lengths become much smaller compared with those of inflow. The relationship of RMS (root mean square) of wake-flow and the mean wind speed of inflow is approximately linear. The special structures of wake-flow in time-frequency domain are also analyzed using wavelet transform, which aids to reveal the forming process of wake-flow.

DNA barcoding and phylogenetic analysis of midges belonging to Culicoides (Diptera: Ceratopogonidae) subgenus Hoffmania in Yunnan, China

Duan Ying Liang,Bellis Glenn,Yang Zhen Xing,Li Zhan Hong,Liu Bing Gang,Li Le 한국응용곤충학회 2022 Journal of Asia-Pacific Entomology Vol.25 No.4

DNA barcodes obtained from cytochrome c oxidase subunit 1 (cox1) offer a fast and easy way to identify a range of biological organisms. Culicoides (Diptera: Ceratopogonidae) are a group of small, blood sucking midges whose species are the vectors for some arboviruses, such as bluetongue virus, African horse sickness virus, epizootic hemorrhagic disease virus and equine encephalosis virus. Identification of these small insects is difficult so constructing DNA barcode libraries for species present in certain areas is helpful to clarify the taxonomy and assist non-specialist workers to identify species. In this study, we analysed specimens belonging to C. subgenus Hoffmania collected from 12 towns of Yunnan Province, China. Specimens were identified by morphology and processed to construct DNA barcodes. A total of 185 specimens referable to 6 morphological species were pro cessed for cox1 and 28S rRNA sequencing. The resulting 185 cox1 sequences were assigned to 13 barcode index numbers (BINs) which include 9 novel BINs. Molecular and morphological evidence was used to support the transfer of 4 species previously assigned to C. subg. Avaritia into C. subg. Hoffmania. Molecular analysis revealed the presence of 7 potential cryptic species within C. innoxius, three within C. liui and two within C. insignipennis.

Electric Field Finite Element Analysis and Experimentation of Plate-Plate Type Electrospinning Machine

Duan Hong-wei,Jiang Jin-gang,Li Bo-yang,Li Bin,He Tian-hua 보안공학연구지원센터 2014 International Journal of Control and Automation Vol.7 No.7

MEMD Interval Threshold Filter and Twin SVM for Electromagnetic Template Attack

Duan Li,Hong-xin Zhang,Qiang Li,Xinjie Zhao,Pengfei He 보안공학연구지원센터 2016 International Journal of Signal Processing, Image Vol.9 No.11

To overcome the dependence on prior knowledge of traditional filtering algorithm, this paper proposes a novel non-parameter and adaptive multivariate empirical mode decomposition interval threshold (MEMD-IT) denoising approach for signal preprocessing of electromagnetic template attack(ETA). MEMD-IT can reduce the discontinuity induced by traditional MEMD-DT and aims to remove the Gaussian noise coupled into side-channel electromagnetic radiations. The proposed method and some other filters such as butterworth low-pass filter(BLPF),wavelet threshold denoising and MEMD direct threshold (MEMD-DT) denoising are applied to analyze the electromagnetic radiation traces intercepted while cipher device was implementing RC4 encryption algorithm. Furthermore, twin SVM multi-class classifier based ETA was performed to evaluate the attack results. In the same attack scenario, the highest predictive success rate for 9 Hamming Weights of the key reached 92%,90%,84%,83% and 73% for MEMD-IT, WFTF, MEMD-DT,WULETF and BLPF preprocessing methods, respectively. The experiment results indicate that our proposed scheme has a significant performance compared with the traditional ETA.