1.Brassica juncea WRKY12 mediates bolting and flowering by interacting with the SOC1 and FUL promoters.
Yifang HUANG ; Yue DONG ; Yue YU ; Dakun LIU ; Qinlin DENG ; Yuanda WANG ; Dayong WEI ; Zhimin WANG ; Qinglin TANG
Chinese Journal of Biotechnology 2025;41(7):2818-2828
Flowering and bolting are important agronomic traits in cruciferous crops such as Brassica juncea. Timely flowering can ensure the crop organ yield and quality, as well as seed propagation. The WRKY family plays an important role in regulating plant bolting and flowering, while the function and mechanism of WRKY12 in B. juncea remain unknown. To explore its function and mechanism in bolting and flowering of B. juncea, we cloned and characterized the BjuWRKY12 gene in B. juncea and found that its expression levels were significantly higher in flowers and inflorescences than in leaves. BjuWRKY12 belonged to the Ⅱc subfamily of the WRKY family, and subcellular localization indicated that the protein was located in the nucleus. Ectopic overexpression of BjuWRKY12 in transgenic lines promoted bolting and flowering, leading to significant increases in the expression levels of flowering integrators SOC1 and FUL. Furthermore, yeast one-hybrid and dual luciferase reporter system assays confirmed that BjuWRKY12 directly bound to the promoters of BjuSOC1 and BjuFUL, undergoing protein-DNA interactions. This discovery gives new insights into the regulation network and molecular mechanisms of BjuWRKY12, laying a theoretical foundation for the breeding of high-yield and high-quality varieties of B. juncea.
Mustard Plant/metabolism*
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Flowers/growth & development*
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Plant Proteins/physiology*
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Promoter Regions, Genetic/genetics*
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Gene Expression Regulation, Plant
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Plants, Genetically Modified/genetics*
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Transcription Factors/metabolism*
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MADS Domain Proteins/metabolism*
2.Virtual screening of active ingredients of traditional Chinese medicine in treating COVID-19 based on molecular docking and molecular dynamic simulation.
Minghao LIU ; Iqbal Khan FAEZ ; Yuqing XIAO ; Xu WANG ; Ziran HU ; Dakun LAI
Journal of Biomedical Engineering 2022;39(5):1005-1014
We aim to screen out the active components that may have therapeutic effect on coronavirus disease 2019 (COVID-19) from the severe and critical cases' prescriptions in the "Coronavirus Disease 2019 Diagnosis and Treatment Plan (Trial Ninth Edition)" issued by the National Health Commission of the People's Republic of China and explain its mechanism through the interactions with proteins. The ETCM database and SwissADME database were used to screen the active components contained in 25 traditional Chinese medicines in 3 prescriptions, and the PDB database was used to obtain the crystal structures of 4 proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Molecular docking was performed using Autodock Vina and molecular dynamics simulations were performed using GROMACS. Binding energy results showed that 44 active ingredients including xambioona, gancaonin L, cynaroside, and baicalin showed good binding affinity with multiple targets of SARS-CoV-2, while molecular dynamics simulations analysis showed that xambioona bound more tightly to the nucleocapsid protein of SARS-CoV-2 and exerted a potent inhibitory effect. Modern technical methods are used to study the active components of traditional Chinese medicine and show that xambioona is an effective inhibitor of SARS-CoV-2 nucleocapsid protein, which provides a theoretical basis for the development of new anti-SARS-CoV-2 drugs and their treatment methods.
Humans
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SARS-CoV-2
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Molecular Docking Simulation
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Medicine, Chinese Traditional
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Molecular Dynamics Simulation
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Nucleocapsid Proteins
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Antiviral Agents/pharmacology*
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COVID-19 Drug Treatment
3.Automatic epileptic seizure detection algorithm based on dual density dual tree complex wavelet transform.
Tongzhou KANG ; Rundong ZUO ; Lanfeng ZHONG ; Wenjing CHEN ; Heng ZHANG ; Hongxiu LIU ; Dakun LAI
Journal of Biomedical Engineering 2021;38(6):1035-1042
It is very important for epilepsy treatment to distinguish epileptic seizure and non-seizure. In this study, an automatic seizure detection algorithm based on dual density dual tree complex wavelet transform (DD-DT CWT) for intracranial electroencephalogram (iEEG) was proposed. The experimental data were collected from 15 719 competition data set up by the National Institutes of Health (NINDS) in Kaggle. The processed database consisted of 55 023 seizure epochs and 501 990 non-seizure epochs. Each epoch was 1 second long and contained 174 sampling points. Firstly, the signal was resampled. Then, DD-DT CWT was used for EEG signal processing. Four kinds of features include wavelet entropy, variance, energy and mean value were extracted from the signal. Finally, these features were sent to least squares-support vector machine (LS-SVM) for learning and classification. The appropriate decomposition level was selected by comparing the experimental results under different wavelet decomposition levels. The experimental results showed that the features selected in this paper were different between seizure and non-seizure. Among the eight patients, the average accuracy of three-level decomposition classification was 91.98%, the sensitivity was 90.15%, and the specificity was 93.81%. The work of this paper shows that our algorithm has excellent performance in the two classification of EEG signals of epileptic patients, and can detect the seizure period automatically and efficiently.
Algorithms
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Electroencephalography
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Epilepsy/diagnosis*
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Humans
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Seizures/diagnosis*
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Signal Processing, Computer-Assisted
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Support Vector Machine
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Wavelet Analysis
4.Diagnostic value of acoustic radiation force impulse imaging for evaluating the degree of liver fibrosis in chronic hepatitis B
Min CHEN ; Dakun ZHANG ; Yang LIU ; Ruifang WANG ; Xiaoyu DONG ; Zhiyan LI
Chinese Journal of Ultrasonography 2015;(4):311-315
Objective To investigate the clinical value of the acoustic radiation force impulse imaging (ARFI) in the quantitative evaluation of fibrosis staging in chronic hepatitis B .Methods A total of 373 patients with chronic hepatitis B were grouped in accordance with the depth of the right anterior lobe and posterior lobe of the liver and underwent ARFI to measure ARFI values .Liver biopsy was performed in all patients to investigate the relationship between liver fibrosis stages and ARFI values in different groups . Results The ARFI values in different pathological grades with the same depth of the right anterior and right posterior lobe of the liver were statistically significant ( P < 0 0.01);the ARFI values between the middle and deep parts of the right anterior lobe and the same location of the right posterior lobe were statistically significant ( P <0 0.1);for the right anterior lobe ,the ARFI value of the shallow part showed statistical significance from that of the middle and the deep part ( P < 0 0.5 ) .Receiver operating characteristic (ROC) curve analysis for different sampling locations showed that the largest area under the ROC curve ,which was 0 8.18 ,existed in the middle part of the right anterior lobe ,indicating that it could be the optimal sampling location for the measurement of ARFI values .Liver stiffness at ARFI imaging was significantly correlated with liver fibrosis stage in chronic hepatitis B and spearman coefficient of correlation was 0 5.30 ( P <0 0.01) .The areas under the ROC curves for the chronic hepatitis B patients with severe liver fibrosis (≥ S3) and early cirrhosis (= S4) were 0 8.18 and 0 8.60 ,respectively .Conclusions ARFI imaging was promising for clinical application and could be utilized as a noninvasive method for the quantitative evaluation of fibrosis staging in chronic hepatitis B .
5.Effect of peroxisome proliferator-activated receptor-γ on endothelial cells oxidative stress induced by Porphyromonas gingivalis
Peng LI ; Meng WAN ; Jianru LIU ; Liangzhong LI ; Dakun ZHANG
Journal of Peking University(Health Sciences) 2015;47(6):977-982
Objective:To detect the degree of oxidative stress in the process when Porphyromonas gin-givalis ( P. gingivalis) stimulates human vascular endothelium, And to investigate the effect of peroxi-some proliferator-activated receptor(PPAR)γ on oxidative stress during this process. Methods:Human vascular endothelial cells ( HVECs) line EA. hy926 ( American Type Culture Collection ,United States) was cultured in high glucose Dulbecco' s modified eagle medium ( DMEM) . Four groups were designed:control group, P. gingivalis infected group, PPARγactivated group and PPARγblocked group. In con-trol group HVECs were cultured with only DMEM. In P. gingivalis infected group, HVECs were time-dependently stimulated by P. gingivalis W83 from 0 to 12 h. In PPARγ activated group or PPARγblocked group, PPARγ was pre-activated or blocked by a representative PPARγ agonist(15d-PGJ2 10μmol/L) or antagonist ( GW966210μmol/L) 30 minutes before the cells were stimulated by P. gingiva-lis. At 0, 0. 5, 1, 1. 5, 2, 4, 8, and 12 h, the culture medium was collected individually and centri-fuged, and the supernatant was stored for assay. Glutathione peroxidase (GSH-PX) and malondialdehyde( MDA) were analysed by enzyme-linked immunosorbent assay. Cellular reactive oxygen species ( ROS) were detected through 2',7'-dichlorofluorescin diacetate (DCFA-DA) fluorescent probe at various time points of the different groups. Results:In P. gingivalis infected group, the levels of GSH-PX [(5. 56 ± 0. 97) μmol/L] and MDA [(0. 84 ± 0. 18) nmol/L] were significantly higher than those in control group [GSH-PX(4. 71 ± 0. 64) μmol/L, MDA (0. 59 ± 0. 18) nmol/L)]. The levels of GSH-PX and MDA in PPARγactivated group [GSH-PX (5. 38 ± 0. 84) μmol/L, MDA (0. 84 ± 0. 22) nmol/L] and in PPARγblocked group [GSH-PX (5. 37 ± 0. 76) μmol/L, MDA (0. 85 ± 0. 14) nmol/L] were signi-ficantly higher than those in control group (P <0. 05). In the PPARγ activated group, the levels of GSH-PX at 0 . 5 and 8 h were significantly higher than those from 1 . 5 h to 4 h ( P<0 . 05 ) , while no difference was observed on the MDA levels at different time points. There was no significant difference at various time points for the levels of GSH-PX and MDA in PPARγ blocked group. The level of cellular ROS detected by DCFH-DA in P. gingivalis infected group was significantly higher than that in control group (10 108. 65 ± 1 805. 18 vs. 6 049. 06 ± 1 199. 19,P<0. 05). No difference was observed be-tween PPARγ activated group (7 120. 94 ± 1 447. 30) or PPARγblocked group (6 727. 35 ± 1 483. 68) and control group. Conclusion:Oxidative stress happens when P. gingivalis stimulates human vascular endothelium. PPARγ may involve in modulating oxidative stress during this process.
6.Contrast enhanced ultrasound features of hepatic tumors contained lipid:comparing with MRI ifndings
Yang, LIU ; Enze, QU ; Zhiyan, LI ; Yuejuan, GAO ; Min, CHEN ; Dakun, ZHANG
Chinese Journal of Medical Ultrasound (Electronic Edition) 2014;(3):29-32
Objective To summarize the imaging features of hepatic tumors contained lipid by contrast enhanced ultrasound (CEUS), and compare with MRI ifndings. Methods From July 2010 to December 2012, 17 patients of hepatocellular carcinoma containing lipid component in the 302nd Hospital of the People′s Liberation Army underwent dual-echo sequence MRI imaging. Fifteen patients were conifrmed by enhanced MRI and contrast-enhanced CT, while the other 2 patients were confirmed by pathology. The features of ultrasonography, CEUS and MRI were analyzed. Kappa analysis test was analyzed for the consistency of CEUS and MRI ifndings. Results In the two-dimensional ultrasound of 17 lesions, 9 were hypoechoic heterogeneous lesions, 5 were hypoechoic lesions;13 lesions with clear boundaries, 4 lesions with unclear boundaries;peripheral blood lfow signal in 5 lesions and rich blood lfow in 1 lesion were observed by color Doppler ultrasound, 11 lesions had no signiifcant blood lfow signal;15 lesions showed fast high enhancement in CEUS arterial phase, 1 lesion with synchronization enhancement, 1 lesion with mild enhancement;10 lesions showed portal clearance, 1 lesion showed an enhanced synchronization, 1 lesion with mild enhancement;16 lesions showed clearance in delay phase, 1 enhanced lesion showed isoenhancement;6 lesions presented intra-lesion or surrounding patchy, irregular non-enhancement areas. CEUS diagnostic accuracy was 82%(14/17), the diagnostic accuracy of MRI was 88%(15/17). The Kappa consistency test was 0.628, while CEUS and MRI results were in good agreement. Conclusions Performance of hepatocellular lipid-containing ultrasound contrast arterial phase shows non-enhancement areas. Contrast enhanced ultrasound features of lipid-containing hepatocellular carcinoma are valuable for the clinical diagnois.
7.Clinical value of acoustic radiation force impulse imaging and APRI for quantitative evaluating the degree of liver fibrosis in chronic hepatitis C patients
Dakun ZHANG ; Min CHEN ; Yang LIU ; Ruifang WANG ; Zhiyan LI ; Xiaoyu DONG ; Guangde ZHOU
Chinese Journal of Ultrasonography 2013;(1):30-33
Objective To investigate the diagnostic value of the acoustic radiation force impulse (ARFI) technology and AST/PLT ratio index (APRI) for the assessment of the liver fibrosis in chronic hepatitis C patients.Methods 107 patients with chronic hepatitis C were included,the subjects were underwent liver biopsy,liver function,blood count,as well as real-time acoustic elastography examination.The APRI was calculated according the following formula,APRI =AST (ULN)/PLT (109/L).ARFI and APRI were compared by correlation with liver fibrosis stage in chronic hepatitis C.Referring to the histologic fibrosis stage on liver biopsy,all the ARFI and the APRI value were assessed by using ROC curve analysis.The corresponding cut-off values,sensitivity and specificity were also calculated and compared.Results The mean values of ARFI and APRI were (1.26 ± 0.27)m/s and 0.30 ± 0.46 for the patients with S1,(1.45 ± 0.51)m/s and 0.29 ± 0.21 for those with S2,(2.03 ± 0.54) m/s and 0.59 ± 0.56 for those with S3,(2.29 ± 0.82) m/s and 0.63 ± 0.35 for those with S4,respectively.ARFI (r =0.61,P <0.001) had a better correlation with liver fibrosis stage in chronic hepatitis C than APRI (r =0.49,P <0.001).Cut-off points of ARFI and APRI were 1.529 m/s and 0.170 for S≥2,1.780 m/s and 0.277 for S≥3,1.780 m/s and 0.446 for S =4,respectively.Accordingly,the areas under the ROC curves for ARFI and APRI were 0.779 and 0.724 for S≥2,0.866 and 0.786 for S≥3,0.790 and 0.779 for S=4,respectively.Conclusions As a non-invasive technology,ARFI is more accurate when applied to evaluate liver fibrosis in patients with chronic hepatitis C than APRI.ARFI technology has potential value for quantitatme evaluation of the liver fibrosis for chronic hepatitis C.
8.Contrast-enhanced ultrasound for differential diagnosis of hyperechoic liver lesions
Liping LIU ; Baowei DONG ; Xiaoling YU ; Xin LI ; Jibin LIU ; Yang WANG ; Hua LI ; Dakun ZHANG
Chinese Journal of Ultrasonography 2008;17(4):315-318
Objective To assess the value of contrast-enhanced ultrasound(US)in differential diagnosis of hyperechoic hepatic lesions when compared to conventional US.Methods Eighty-four hyperechoic liver lesions in 66 patients were examined using both conventional and contrast-enhanced US techniques.Results Receiver operating characteristic analysis revealed a significant improvement in the discrimination of malignant versus benign hyperechoic hepatic lesions (area under the receiver operating characteristic curve,0.867±0.045 at conventional US,0.997±0.003 with contrast-enhanced US(P<0.0001).For correct diagnoses types of hyperechoic liver lesions,contrast-enhanced US improved from 64.3% to 92.9%,comic)ared with conventional US (P<0.001).Conclusions Contrast-enhanced US showed a significant improvement in characterization and differentiation of hyperechoic hepatic lesions when compared to conventional US.
9.Application of computer to medical ultrasound images
Yibing LI ; Dakun YU ; Xiaodong LIU
Chinese Medical Equipment Journal 1989;0(04):-
This paper introduces the application of computer to medical ultrasound images in which the processing of medical ultrasound images and picture archiving and communication system(PACS) are involved in.

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