Transcriptome and digital gene expression analysis of herbaceous peony (Paeonia lactiflora Pall.) to screen thermo-tolerant related differently expressed genes

Jun Tao,Zhaojun Hao,Mengran Wei,Saijie Gong,Daqiu Zhao 한국유전학회 2016 Genes & Genomics Vol.38 No.12

Herbaceous peony (Paeonia lactiflora Pall.) is easily injured by heat stress (HS), which greatly restricts its application and promotion. In this study, the thermo-tolerance of three representative P. lactiflora cultivars had been firstly assessed. ‘Zifengyu’ was identified as the thermo-tolerant cultivar with relatively lower values and smaller variations in malondialdehyde, hydrogen peroxide (H2O2) and proline contents under HS. Subsequently, their transcriptomes were sequenced by RNA sequencing (RNAseq) technology to construct a complete database. 81,599 unigenes were obtained, and 34,940 unigenes had been annotated. Moreover, through digital gene expression analysis of thermo-tolerant ‘Zifengyu’ and moderately thermo-tolerant ‘Hongyanzhenghui’, 161 heat stress response genes had been screened involving heat shock protein genes, plant hormone signal transduction related genes, fatty acid synthesis genes, reactive oxygen speciesscavenging genes and secondary metabolites related genes. And the effectively and timely response of these genes to HS could endow thermo-tolerance to ‘Zifengyu’. Among these genes, 11 key thermo-tolerant related genes whose expressions were all significantly up-regulated in ‘Zifengyu’ and ‘Hongyanzhenghui’ during development and the former possessed higher levels could be regarded as the candidate genes, including isoprene synthase gene, 2 peroxidase genes, 3-oxoacyl-acyl carrier protein reductase gene (FabG), 3 transcription factor genes (bHLH, NAC and WRKY), HSP20 and 3 HSP70. These results could provide a better understanding of heat stress response in P. lactiflora, and pave for the breeding of thermo-tolerant cultivars.

Effects of tryptophan and phenylalanine on tryptophol production in Saccharomyces cerevisiae revealed by transcriptomic and metabolomic analyses

Gong Xiaowei,Luo Huajun,Hong Liu,Wu Jun,Wu Heng,Song Chunxia,Zhao Wei,Han Yi,Dao Ya,Zhang Xia,Zhu Donglai,Luo Yiyong 한국미생물학회 2022 The journal of microbiology Vol.60 No.8

Tryptophol (TOL) is a metabolic derivative of tryptophan (Trp) and shows pleiotropic effects in humans, plants and microbes. In this study, the effect of Trp and phenylalanine (Phe) on TOL production in Saccharomyces cerevisiae was determined, and a systematic interpretation of TOL accumulation was offered by transcriptomic and metabolomic analyses. Trp significantly promoted TOL production, but the output plateaued (231.02−266.31 mg/L) at Trp concentrations ≥ 0.6 g/L. In contrast, Phe reduced the stimulatory effect of Trp, which was strongly dependent on the Phe concentration. An integrated genomic, transcriptomic, and metabolomic analysis revealed that the effect of Trp and Phe on TOL production was mainly related to the transamination and decarboxylation of the Ehrlich pathway. Additionally, other genes, including thiamine regulon genes (this), the allantoin catabolic genes dal1, dal2, dal4, and the transcriptional activator gene aro80, may play important roles. These findings were partly supported by the fact that the thi4 gene was involved in TOL production, as shown by heterologous expression analysis. To the best of our knowledge, this novel biological function of thi4 in S. cerevisiae is reported here for the first time. Overall, our findings provide insights into the mechanism of TOL production, which will contribute to TOL production using metabolic engineering strategies.

Genome-Wide Identification and Functional Analysis of Long Non-coding RNAs in Sesame Response to Salt Stress

Gong Huihui,You Jun,Zhang Xiurong,Liu Yanzhong,Zhao Fengtao,Cui Xinxiao,Zhang Yujuan 한국식물학회 2021 Journal of Plant Biology Vol.64 No.6

Long non-coding RNAs (lncRNAs) play important roles in various biological regulatory processes in which complicated mechanisms are involved, as well as stress-responsive regulation. However, the number, characteristics, sequences and possible effects of lncRNAs in sesame response to salt stress are poorly understood. In this study, a total of 2482 lncRNAs were identified from two contrasting sesame genotypes under salt stress using high-throughput RNA sequencing, of which 599 were intergenic lncRNAs, 293 were antisense lncRNAs and 786 lncRNAs may encode proteins. Expression pattern analysis showed that most lncRNAs were expressed at a low level and a total of 700 differentially expressed lncRNAs were characterized as salt responsive in sesame. A large number of potential target genes of lncRNAs were predicted, and functional annotation analysis indicated that the differentially expressed lncRNAs in salt stress may regulate protein-coding genes involved in several important pathways related to glycolysis/gluconeogenesis, flavonoid biosynthesis, monoterpenoid biosynthesis, biotin metabolism, galactose metabolism, cyanoamino acid metabolism and carotenoid biosynthesis. Integrated analysis of lncRNAs and mRNAs revealed the regulatory role of lncRNAs associated with salt resistance in sesame, and provided convincing proof of the interplay of specific candidate target genes with lncRNAs. Our results indicated that a comprehensive set of lncRNAs with potential target genes were responsive to salt stress in sesame seedlings. These findings provided important information on salinity responses and adaptation of sesame to salt stress and may constitute useful resources for more comprehensive studies on gene regulation in sesame.

Specific Mutations in APC, with Prognostic Implications in Metastatic Colorectal Cancer

Huan Peng,Jun Ying,Jia Zang,Hao Lu,Xiaokai Zhao,Pengmin Yang,Xintao Wang,Jieyi Li,Ziying Gong,Daoyun Zhang,Zhiguo Wang 대한암학회 2023 Cancer Research and Treatment Vol.55 No.4

Purpose Loss-of-function mutations in the adenomatous polyposis coli (APC) gene are common in metastatic colorectal cancer (mCRC). However, the characteristic of APC specific mutations in mCRC is poorly understood. Here, we explored the clinical and molecular characteristics of N-terminal and C-terminal side APC mutations in Chinese patients with mCRC. Materials and Methods Hybrid capture-based next-generation sequencing was performed on tumor tissues from 275 mCRC pati-ents to detect mutations in 639 tumor-associated genes. The prognostic value and gene-pathway difference between APC specific mutations in mCRC patients were analyzed. Results APC mutations were highly clustered, accounting for 73% of all mCRC patients, and most of them were truncating mutations. The tumor mutation burden of the N-terminal side APC mutations group (n=76) was significantly lower than that of the C-terminal side group (n=123) (p < 0.001), further confirmed by the public database. Survival analysis showed that mCRC patients with N-terminus side APC mutations had longer overall survival than C-terminus side. Tumor gene pathway analysis showed that gene mutations in the RTK/RAS, Wnt and transforming growth factor β signaling pathways of the C-terminal group were significantly higher than those of the N-terminal group (p < 0.05). Additionally, KRAS, AMER1, TGFBR2, and ARID1A driver mutations were more common in patients with C-terminal side APC mutations. Conclusion APC specific mutations have potential function as mCRC prognostic biomarkers. There are obvious differences in the gene mutation patterns between the C-terminus and N-terminus APC mutations group, which may have certain guiding significance for the subsequent precise treatment of mCRC.

Down-regulation of miRNA-452 is Associated with Adriamycin-resistance in Breast Cancer Cells

Hu, Qing,Gong, Jian-Ping,Li, Jian,Zhong, Shan-Liang,Chen, Wei-Xian,Zhang, Jun-Ying,Ma, Teng-Fei,Ji, Hao,Lv, Meng-Meng,Zhao, Jian-Hua,Tang, Jin-Hai Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.13

Adriamycin (ADR) is an important chemotherapeutic agent frequently used in treatment of breast cancer. However, resistance to ADR results in treatment failure in many patients. Recent studies have indicated that microRNAs (miRNAs) may play an important role in such drug-resistance. In the present study, microRNA-452 (miR-452) was found to be significantly down-regulated in adriamycin-resistant MCF-7 cells (MCF-7/ADR) compared with the parental MCF-7 cells by miRNA microarray and real-time quantitative PCR (RT-qPCR). MiR-452 mimics and inhibitors partially changed the adriamycin-resistance of breast cancer cells, as also confirmed by apoptosis assay. In exploring the potential mechanisms of miR-452 in the adriamycin-resistance of breast cancer cells, bioinformatics analysis, RT-qPCR and Western blotting showed that dysregulation of miR-452 played an important role in the acquired adriamycin-resistance of breast cancer, maybe at least in part via targeting insulin-like growth factor-1 receptor (IGF-1R).

Performance study of g-C3N4/carbon black/BiOBr@Ti3C2/MoS2 photocatalytic fuel cell for the synergistic degradation of different types of pollutants

Guo Huilin,Yu Tingting,Zhao Lei,Qian Jun,Yu Jiahe,Zhang Yu,Teng Yongyue,Zhu Chunshui,Yang Tao,Chen Wenbin,Gong Picheng,Jiang Cuishuang,Gao Changfei,Yang Bing,Yang Chenyu 한국탄소학회 2023 Carbon Letters Vol.33 No.3

In this study, a bipolar visible light responsive photocatalytic fuel cell (PFC) was constructed by loading a Z-scheme g-C3N4/carbon black/BiOBr and a Ti3C2/MoS2 Schottky heterojunction on the carbon brush to prepare the photoanode and photocathode, respectively. It greatly improved the electron transfer and achieved efficient degradation of organic pollutants such as antibiotics and dyes simultaneously in two chambers of the PFC system. The Z-scheme g-C3N4/carbon black/BiOBr formed by adding highly conductive carbon black to g-C3N4/BiOBr not only effectively separates the photogenerated carriers, but also simultaneously retains the high reduction of the conduction band of g-C3N4 and the high oxidation of the valence band of BiOBr, improving the photocatalytic performance. The exceptional performance of Ti3C2/MoS2 Schottky heterojunction originated from the superior electrical conductivity of Ti3C2 MXene, which facilitated the separation of photogenerated electron–hole pairs. Meanwhile, the synergistic effect of the two photoelectrodes further improved the photocatalytic performance of the PFC system, with degradation rates of 90.9% and 99.9% for 50 mg L−1 tetracycline hydrochloride (TCH) and 50 mg L−1 rhodamine-B (RhB), respectively, within 180 min. In addition, it was found that the PFC also exhibited excellent pollutant degradation rates under dark conditions (79.7%, TCH and 97.9%, RhB). This novel pollutant degradation system is expected to provide a new idea for efficient degradation of multiple pollutant simultaneously even in the dark.

A novel method for longitudinal modification and tooth contact analysis of non-circular cylindrical gears

Dawei Li,Yongping Liu,Jun Gong,Yongqiao Wei,Gang Zhao 대한기계학회 2022 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.36 No.12

The traditional geometry of non-circular cylindrical gears provides a contact line between tooth surfaces. In a misaligned non-circular cylindrical gear drive, causing edge contacts that result in noise and vibration. The point contact of the tooth surface is achieved by modification of the driving gear in the longitudinal direction, in order to reduce the sensitivity of tooth surface contact to installation errors. The proposed longitudinal modification method is based on the application of a grinding worm by controlling the center distance of non-circular cylindrical gear and worm. Based on the gear meshing principle, a mathematical model of the tooth surfaces of non-circular cylindrical gears is established, and a parametric tooth surface equation with a unified expression is obtained. Tooth contact analysis (TCA) of non-circular cylindrical gears shows that the contact path and contact area on the tooth surface are shifted with the change of installation error, but still distributed in the middle of the tooth surface without creating edge contact. The transmission error is increased with the growth of installation error. Tooth modification in a longitudinal direction has an obvious improvement effect on the bad tooth contact condition, but too large a tooth modification parameter will make the tooth surface load distribution concentrated in a smaller area, which results in the decrease of gear load capacity.

An Effective Guidewire Looping Technique for the Recanalization of Occlusive Segments of Infrapopliteal Vessels

Jian-bo Wang,Jun-gong Zhao,Ming-hua Li,Yue-qi Zhu,Jue Wang,Pei-lei Zhang 대한영상의학회 2010 Korean Journal of Radiology Vol.11 No.4

Objective: To determine the efficacy, safety and primary follow-up results of a guidewire looping technique for the treatment of infrapopliteal arteries. Materials and Methods: From October 2006 to May 2008, an intraluminal angioplasty of the infrapopliteal arteries was attempted in 200 consecutive patients. Altogether, 417 infrapopliteal lesions, with lengths varying from 2 cm to 32 cm, were treated as part of this study, including 305 lesions in the anterior tibial arteries, 89 in the posterior tibial arteries, and 23 in the peroneal arteries. The ‘U’-shaped guidewire technique was attempted in 393 lesions from 361 limbs. The tip of a hydrophilic 0.035-inch guidewire was formed into a ‘U’ shape with the aid of a 4-Fr catheter and collateral branch vessel to recanalize the completely occluded long segment lesions. Results: A successful angioplasty with at least one artery recanalized directly to the malleolar or dorsal foot was achieved in 322 limbs (89%). The looping technique had a success rate of 90% (352 of 393 lesions). After the procedure, the rest pain was relieved in 58 of 69 patients, while 207 of 245 limbs (85%) showed improvement for intermittent claudication. Complete wound healing was noted in 21 of 54 patients, while 20 of 54 patients showed an improvement in the wound size or depth. A total of 38 major immediate procedure-related complications were noted, including retroperitoneal hematoma, distal emboli, and vessel rupture. Conclusion: The results of this study suggests that the guidewire looping technique is a safe and effective method for the recanalization of the occluded lesions in infrapopliteal vessels. Objective: To determine the efficacy, safety and primary follow-up results of a guidewire looping technique for the treatment of infrapopliteal arteries. Materials and Methods: From October 2006 to May 2008, an intraluminal angioplasty of the infrapopliteal arteries was attempted in 200 consecutive patients. Altogether, 417 infrapopliteal lesions, with lengths varying from 2 cm to 32 cm, were treated as part of this study, including 305 lesions in the anterior tibial arteries, 89 in the posterior tibial arteries, and 23 in the peroneal arteries. The ‘U’-shaped guidewire technique was attempted in 393 lesions from 361 limbs. The tip of a hydrophilic 0.035-inch guidewire was formed into a ‘U’ shape with the aid of a 4-Fr catheter and collateral branch vessel to recanalize the completely occluded long segment lesions. Results: A successful angioplasty with at least one artery recanalized directly to the malleolar or dorsal foot was achieved in 322 limbs (89%). The looping technique had a success rate of 90% (352 of 393 lesions). After the procedure, the rest pain was relieved in 58 of 69 patients, while 207 of 245 limbs (85%) showed improvement for intermittent claudication. Complete wound healing was noted in 21 of 54 patients, while 20 of 54 patients showed an improvement in the wound size or depth. A total of 38 major immediate procedure-related complications were noted, including retroperitoneal hematoma, distal emboli, and vessel rupture. Conclusion: The results of this study suggests that the guidewire looping technique is a safe and effective method for the recanalization of the occluded lesions in infrapopliteal vessels.

Research on Human-robot Shared Control of Throat Swab Sampling Robot Based on Intention Estimation

Ying-Long Chen,Fu-Jun Song,Peng-Yu Zhao,Yong-Jun Gong,Heng-Fei Yan 제어·로봇·시스템학회 2024 International Journal of Control, Automation, and Vol.22 No.2

With the spread and persistence of COVID-19, pharyngeal swab sampling, is an important link in nucleic acid testing, which is characterized by a high workload and susceptibility to infection. Therefore, it is necessary for medical workers to use medical robots instead of manual site sampling for collaborative sampling. However, the traditional teleoperation has difficulty ensuring the closed-loop performance due to the delay of the actual process, along with the weak control performance; Moreover, a robot cannot accurately plan and track sampling paths due to sensor accuracy and the changes in patient pharyngeal posture. The paper proposes a human-robot shared control strategy based on intention estimation, introducing the human intention as a reference, and the operator and robot work together to solve various significant problems during sampling. The human-robot negotiation based on the method includes the human judgement and perception and the robot into the invasion task. Through, the shared control based on the operator intention estimation, the robot can operate the obstacle avoidance and approach the target contact point remotely. Finally, two kinds of experiments of invasion process of throat swab sampling are implemented: a static target invasive experiment and a dynamic target invasive experiment, aiming at two different sampling conditions. Compared with the robotic independent control sampling, the time consumption in the two experiments is reduced by 34.8% and 41.6%, respectively, and the ultimate target position is basically within the scope of sampling field (where the range of the posterior pharynx wall < 20 mm). Thus, the sampling rate can reach 100%. Compared with independent control sampling by humans, the time consumption of the two experiments is respectively reduced by 15.9% and 42.3% on average, and the target position accuracy and sampling rate are quite close. Experimental results show that the control strategy improves the speed, flexibility, and intelligence of task execution compared to common sampling methods, laying the foundation for low-cost human-robot collaborative sampling.

Suppression of CDK2 expression by siRNA induces cell cycle arrest and cell proliferation inhibition in human cancer cells

( Xiang E Long ),( Zhao Hui Gong ),( Lin Pan ),( Zhi Wei Zhong ),( Yan Ping Le ),( Qiong Liu ),( Jun Ming Guo ),( Jiu Chang Zhong ) 한국생화학분자생물학회 (구 한국생화학회) 2010 BMB Reports Vol.43 No.4

Cyclin-dependent kinase 2 (CDK2) is a member of serine/threonine protein kinases, which initiates the principal transitions of the eukaryotic cell cycle and is a promising target for cancer therapy. The present study was designed to inhibit cdk2 gene expression to induce cell cycle arrest and cell proliferation suppression. Here, we constructed a series of RNA interference (RNAi) plasmids which can successfully express small interference RNA (siRNA) in the transfected human cells. The results showed that the RNAi plasmids containing the coding sequences for siRNAs down-regulated the cdk2 gene expression in human cancer cells at the mRNA and the protein levels. Furthermore, we found that the cell cycle was arrested at G0G1 phases and the cell proliferation was inhibited by different siRNAs. These results demonstrate that suppression of CDK2 activity by RNAi may be an effective strategy for gene therapy in human cancers. [BMB reports 2010; 43(4): 291-296]