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Xu F, Dong H, Guo W, Le L, Jing Y, Fletcher JC, Sun J, Pu L. The trxG protein ULT1 regulates Arabidopsis organ size by interacting with TCP14/15 to antagonize the LIM peptidase DA1 for H3K4me3 on target genes. Plant Commun 2024; 5:100819. [PMID: 38217289 PMCID: PMC11009162 DOI: 10.1016/j.xplc.2024.100819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/18/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
Plant organ size is an important agronomic trait that makes a significant contribution to plant yield. Despite its central importance, the genetic and molecular mechanisms underlying organ size control remain to be fully clarified. Here, we report that the trithorax group protein ULTRAPETALA1 (ULT1) interacts with the TEOSINTE BRANCHED1/CYCLOIDEA/PCF14/15 (TCP14/15) transcription factors by antagonizing the LIN-11, ISL-1, and MEC-3 (LIM) peptidase DA1, thereby regulating organ size in Arabidopsis. Loss of ULT1 function significantly increases rosette leaf, petal, silique, and seed size, whereas overexpression of ULT1 results in reduced organ size. ULT1 associates with TCP14 and TCP15 to co-regulate cell size by affecting cellular endoreduplication. Transcriptome analysis revealed that ULT1 and TCP14/15 regulate common target genes involved in endoreduplication and leaf development. ULT1 can be recruited by TCP14/15 to promote lysine 4 of histone H3 trimethylation at target genes, activating their expression to determine final cell size. Furthermore, we found that ULT1 influences the interaction of DA1 and TCP14/15 and antagonizes the effect of DA1 on TCP14/15 degradation. Collectively, our findings reveal a novel epigenetic mechanism underlying the regulation of organ size in Arabidopsis.
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Affiliation(s)
- Fan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huixue Dong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Weijun Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Liang Le
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yexing Jing
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jennifer C Fletcher
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Plant Gene Expression Center, United States Department of Agriculture - Agricultural Research Service, Albany, CA 94710, USA
| | - Jiaqiang Sun
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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2
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Liu D, Yan B, Yin Y, Chen F, Guo C, Li Q, Liu J, Pu L, Wu W, Luo J. PI3Kδ Mediates Fibrosis by Patient-Derived Vitreous. J Transl Med 2024; 104:102026. [PMID: 38307209 DOI: 10.1016/j.labinv.2024.102026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/23/2023] [Accepted: 01/24/2024] [Indexed: 02/04/2024] Open
Abstract
The epithelial-mesenchymal transition (EMT) is a fundamental process in developing fibrotic diseases, including forming epiretinal membranes (ERMs). ERMs can result in irreversible vision loss. Previous research has demonstrated that vitreous (VIT) derived from patients with proliferative diabetic retinopathy can stimulate angiogenesis through the Axl/PI3K/Akt pathway. Building upon this knowledge, we aimed to explore the influence of VIT from patients with macular membranes in ARPE-19 cells. Our findings reveal that patient-derived VIT from individuals with macular membranes promotes EMT and phosphoinositide 3-kinase-delta (PI3Kδ) expression in ARPE-19 cells. To elucidate the function of PI3Kδ in the ERM, we conducted experiments involving the knockout of p110δ, a key subunit of PI3Kδ, and observed that its absence hinders EMT induced by patient-derived VIT. Moreover, p110δ depletion reduces cell proliferation and migration in ARPE-19 cells. Remarkably, these effects were further corroborated by applying the p110δ inhibitor idelalisib, which blocks fibrosis in the laser-induced fibrosis model. Collectively, our results propose that p110δ plays a critical role in the progression of ERMs. Consequently, targeting p110δ emerges as a promising therapeutic approach for mitigating fibrosis. These findings contribute to a better understanding of the underlying mechanisms involved in ERM formation and highlight the potential for p110δ-directed antifibrotic therapy in retinal diseases.
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Affiliation(s)
- Dan Liu
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Department of Ophthalmology, Hunan Key Laboratory of Ophthalmology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bin Yan
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yiwei Yin
- Department of Ophthalmology, Hunan Key Laboratory of Ophthalmology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Fang Chen
- Hunan Key Laboratory of Molecular Precision Medicine, Xiangya Hospital and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Cao Guo
- Institute of Medical Sciences, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qin Li
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jia Liu
- School of Medicine, Hunan University of Medicine, Huaihua, Hunan, China
| | - Li Pu
- Department of Ophthalmology, Hunan Key Laboratory of Ophthalmology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wenyi Wu
- Department of Ophthalmology, Hunan Key Laboratory of Ophthalmology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Jing Luo
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
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Zhang D, Gan Y, Le L, Pu L. Epigenetic variation in maize agronomical traits for breeding and trait improvement. J Genet Genomics 2024:S1673-8527(24)00028-6. [PMID: 38310944 DOI: 10.1016/j.jgg.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 02/06/2024]
Abstract
Epigenetics-mediated breeding (Epibreeding) involves engineering crop traits and stress responses through the targeted manipulation of key epigenetic features to enhance agricultural productivity. While conventional breeding methods raise concerns about reduced genetic diversity, epibreeding propels crop improvement through epigenetic variations that regulate gene expression, ultimately impacting crop yield. Epigenetic regulation in crops encompasses various modes, including histone modification, DNA modification, RNA modification, non-coding RNA, and chromatin remodeling. This review summarizes the epigenetic mechanisms underlying major agronomic traits in maize and identifies candidate epigenetic landmarks in the maize breeding process. We propose a valuable strategy for improving maize yield through epibreeding, combining CRISPR/Cas-based epigenome editing technology and Synthetic Epigenetics (SynEpi). Finally, we discuss the challenges and opportunities associated with maize trait improvement through epibreeding.
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Affiliation(s)
- Daolei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; School of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia 010021, China
| | - Yujun Gan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Liang Le
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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4
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Zang Z, Xu Q, Zhou X, Ma N, Pu L, Tang Y, Li Z. Random forest can accurately predict the technique failure of peritoneal dialysis associated peritonitis patients. Front Med (Lausanne) 2024; 10:1335232. [PMID: 38298506 PMCID: PMC10829598 DOI: 10.3389/fmed.2023.1335232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 12/27/2023] [Indexed: 02/02/2024] Open
Abstract
Instructions Peritoneal dialysis associated peritonitis (PDAP) is a major cause of technique failure in peritoneal dialysis (PD) patients. The purpose of this study is to construct risk prediction models by multiple machine learning (ML) algorithms and select the best one to predict technique failure in PDAP patients accurately. Methods This retrospective cohort study included maintenance PD patients in our center from January 1, 2010 to December 31, 2021. The risk prediction models for technique failure were constructed based on five ML algorithms: random forest (RF), the least absolute shrinkage and selection operator (LASSO), decision tree, k nearest neighbor (KNN), and logistic regression (LR). The internal validation was conducted in the test cohort. Results Five hundred and eight episodes of peritonitis were included in this study. The technique failure accounted for 26.38%, and the mortality rate was 4.53%. There were resignificant statistical differences between technique failure group and technique survival group in multiple baseline characteristics. The RF prediction model is the best able to predict the technique failure in PDAP patients, with the accuracy of 93.70% and area under curve (AUC) of 0.916. The sensitivity and specificity of this model was 96.67 and 86.49%, respectively. Conclusion RF prediction model could accurately predict the technique failure of PDAP patients, which demonstrated excellent predictive performance and may assist in clinical decision making.
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Affiliation(s)
- Zhiyun Zang
- Department of Nephrology, Institute of Nephrology, West China Hospital of Sichuan University, Chengdu, China
| | - Qijiang Xu
- Department of Nephrology, Institute of Nephrology, West China Hospital of Sichuan University, Chengdu, China
- Department of Nephrology, Yibin Second People's Hospital, Yibin, China
| | - Xueli Zhou
- Department of Nephrology, Institute of Nephrology, West China Hospital of Sichuan University, Chengdu, China
| | - Niya Ma
- Department of Nephrology, Institute of Nephrology, West China Hospital of Sichuan University, Chengdu, China
| | - Li Pu
- Department of Nephrology, Institute of Nephrology, West China Hospital of Sichuan University, Chengdu, China
| | - Yi Tang
- Department of Nephrology, Institute of Nephrology, West China Hospital of Sichuan University, Chengdu, China
| | - Zi Li
- Department of Nephrology, Institute of Nephrology, West China Hospital of Sichuan University, Chengdu, China
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Pu L, Yi F, Yu WJ, Li YJ, Tu YH, Xu AH, Wang Y. Endoplasmic reticulum stress mediates environmental particle-induced inflammatory response in bronchial epithelium. J Immunotoxicol 2023; 20:2229428. [PMID: 37417782 DOI: 10.1080/1547691x.2023.2229428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 06/16/2023] [Indexed: 07/08/2023] Open
Abstract
While the detailed mechanisms for how particulate matter (PM) causes adverse health effects in the lungs remain largely unknown, endoplasmic reticulum (ER) stress has been implicated in PM-induced lung injury. The present study was undertaken to examine how/if ER stress might regulate PM-induced inflammation, and to begin to define potential underlying molecular mechanisms. Here, ER stress hallmarks were examined in human bronchial epithelial (HBE) cells exposed to PM. To confirm roles of certain pathways, siRNA targeting ER stress genes and an ER stress inhibitor were employed. Expression of select inflammatory cytokines and related signaling pathway components by the cells were assessed as well. The results showed that PM exposure induced elevations in two ER stress hallmarks, i.e. GRP78 and IRE1α, in time-and/or dose-related manners in the HBE cells. Inhibition of ER stress by siRNA for GRP78 or IRE1α significantly alleviated the PM-induced effects. Further, ER stress appeared to regulate PM-induced inflammation - likely through downstream autophagy and NF-κB pathways - as implied by studies showing that inhibition of ER stress by siRNA of GRP78 or IRE1α caused significant amelioration of PM-induced autophagy and subsequent activation of NF-κB pathways. Moreover, the ER stress inhibitor 4-PBA were used to confirm the protective effects against PM-induced outcomes. Together, the results suggest ER stress plays a deleterious role in PM-induced airway inflammation, possibly through activation of autophagy and NF-κB signaling. Accordingly, protocols/treatments that could lead to inhibited ER stress could potentially be effective for treatment of PM-related airway disorders.
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Affiliation(s)
- Li Pu
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, and Anhui Medical University, Hefei, China
| | - Fen Yi
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, and Anhui Medical University, Hefei, China
| | - Wen-Jing Yu
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, and Anhui Medical University, Hefei, China
| | - Ya-Jing Li
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, and Anhui Medical University, Hefei, China
| | - You-Hui Tu
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, and Anhui Medical University, Hefei, China
| | - Ai-Hui Xu
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, and Anhui Medical University, Hefei, China
| | - Yong Wang
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, and Anhui Medical University, Hefei, China
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Xia X, He X, Pu L, Liu X, Zhou X, Wu XF, Zang Z, Li Z. A randomized controlled comparative study of different fluid exchange modes in urgent-start peritoneal dialysis in patients with end-stage renal disease: automated peritoneal dialysis combined with manual fluid exchange vs. manual fluid exchange alone. Ren Fail 2023; 45:2202756. [PMID: 37313750 DOI: 10.1080/0886022x.2023.2202756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023] Open
Abstract
During urgent-start peritoneal dialysis (USPD) in end-stage renal disease (ESRD) patients, both adequate dialysis and skill training for fluid exchange are essential. However, automated peritoneal dialysis (APD) alone or manual fluid exchange peritoneal dialysis (MPD) alone could meet the above demands. Therefore, our study combined APD with MPD (A-MPD), and compared A-MPD with MPD, aiming to find the most appropriate treatment mode. This was a single-center, prospective, randomized controlled study. All eligible patients were randomized into the MPD and A-MPD groups. All patients underwent a five-day USPD treatment 48 h after catheter implantation, and they were followed up for six months after discharge. Overall, 74 patients were enrolled in this study. Among these, 14 and 60 patients quit due to complications during USPD and completed the study (A-MPD = 31, MPD = 29), respectively. Compared with MPD, the A-MPD treatment mode had a better effect on removing serum creatinine, blood urea nitrogen, and potassium and improving serum carbon dioxide combining power levels; it had less time expenditure on the fluid exchange by nurses (p < 0.05). In addition, patients in the A-MPD group had higher scores on the skill tests than those in the MPD group (p = 0.002). However, no significant differences in short-term peritoneal dialysis (PD) complications, PD technical survival rate, or mortality were found between the two groups. Therefore, the A-MPD mode could be recommended as an adoptable and suitable PD modality for USPD in the future.
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Affiliation(s)
- Xiaoxiao Xia
- Department of Nephrology, Sichuan University, West China Hospital, Chengdu, P.R. China
| | - Xueqin He
- Department of Nephrology, Sichuan University, West China Hospital, Chengdu, P.R. China
- West China School of Nursing, West China Hospital of Sichuan University, Chengdu, P.R. China
| | - Li Pu
- Department of Nephrology, Sichuan University, West China Hospital, Chengdu, P.R. China
- West China School of Nursing, West China Hospital of Sichuan University, Chengdu, P.R. China
| | - Xia Liu
- Department of Nephrology, Sichuan University, West China Hospital, Chengdu, P.R. China
- West China School of Nursing, West China Hospital of Sichuan University, Chengdu, P.R. China
| | - Xueli Zhou
- Department of Nephrology, Sichuan University, West China Hospital, Chengdu, P.R. China
- West China School of Nursing, West China Hospital of Sichuan University, Chengdu, P.R. China
| | - Xiao Fang Wu
- Department of Nephrology, Sichuan University, West China Hospital, Chengdu, P.R. China
- Department of Nephrology, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing, P.R. China
| | - Zhiyun Zang
- Department of Nephrology, Sichuan University, West China Hospital, Chengdu, P.R. China
| | - Zi Li
- Department of Nephrology, Sichuan University, West China Hospital, Chengdu, P.R. China
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Yu J, Song G, Guo W, Le L, Xu F, Wang T, Wang F, Wu Y, Gu X, Pu L. ZmBELL10 interacts with other ZmBELLs and recognizes specific motifs for transcriptional activation to modulate internode patterning in maize. New Phytol 2023; 240:577-596. [PMID: 37583092 DOI: 10.1111/nph.19192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/15/2023] [Indexed: 08/17/2023]
Abstract
Plant height is an important agronomic trait that affects crop yield. Elucidating the molecular mechanism underlying plant height regulation is also an important question in developmental biology. Here, we report that a BELL transcription factor, ZmBELL10, positively regulates plant height in maize (Zea mays). Loss of ZmBELL10 function resulted in shorter internodes, fewer nodes, and smaller kernels, while ZmBELL10 overexpression increased plant height and hundred-kernel weight. Transcriptome analysis and chromatin immunoprecipitation followed by sequencing showed that ZmBELL10 recognizes specific sequences in the promoter of its target genes and activates cell division- and cell elongation-related gene expression, thereby influencing node number and internode length in maize. ZmBELL10 interacted with several other ZmBELL proteins via a spatial structure in its POX domain to form protein complexes involving ZmBELL10. All interacting proteins recognized the same DNA sequences, and their interaction with ZmBELL10 increased target gene expression. We identified the key residues in the POX domain of ZmBELL10 responsible for its protein-protein interactions, but these residues did not affect its transactivation activity. Collectively, our findings shed light on the functions of ZmBELL10 protein complexes and provide potential targets for improving plant architecture and yield in maize.
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Affiliation(s)
- Jia Yu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guangshu Song
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, China
| | - Weijun Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Liang Le
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Fan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ting Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Shangrao Normal University, Shangrao, 334001, China
| | - Fanhua Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yue Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Hu L, He H, Roberts N, Chen J, Yan G, Pu L, Song X, Luo C. Insular dysfunction of interoception in major depressive disorder: from the perspective of neuroimaging. Front Psychiatry 2023; 14:1273439. [PMID: 37840807 PMCID: PMC10568471 DOI: 10.3389/fpsyt.2023.1273439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023] Open
Abstract
Interoception plays a crucial role in maintaining bodily homeostasis and promoting survival, and is considered the basis of human emotion, cognition, and self-formation. A malfunction of interoception is increasingly suggested to be a fundamental component of different mental health conditions, and depressive disorders have been especially closely associated. Interoceptive signaling and processing depends on a system called the "interoceptive pathway," with the insula, located in the deep part of the lateral fissure, being the most important brain structure in this pathway. Neuroimaging studies have revealed alterations in the structure and function of the insula in a large number of individuals with depression, yet the precise relationship between these alterations and interoceptive dysfunction remains unclear. The goal of this review is to examine the evidence that exists for dysfunction of interoception in people with Major Depressive Disorder (MDD), and to determine the associated specific alterations in the structure and function of the insula revealed by neuroimaging. Overall, three aspects of the potential relationship between interoceptive dysfunction and alterations in insular function in people with depression have been assessed, namely clinical symptoms, quantitative measures of interoceptive function and ability, and interoceptive modulation. To conclude, several specific limitations of the published studies and important lines of enquiry for future research are offered.
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Affiliation(s)
- Lan Hu
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China
- The Fourth People’s Hospital of Chengdu, Chengdu, China
| | - Hui He
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China
- The Fourth People’s Hospital of Chengdu, Chengdu, China
| | - Neil Roberts
- Centre for Reproductive Health (CRH), School of Clinical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Jiajia Chen
- The Fourth People’s Hospital of Chengdu, Chengdu, China
| | - Guojian Yan
- The Fourth People’s Hospital of Chengdu, Chengdu, China
| | - Li Pu
- The Fourth People’s Hospital of Chengdu, Chengdu, China
| | - Xufeng Song
- The Fourth People’s Hospital of Chengdu, Chengdu, China
| | - Cheng Luo
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China
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Pu L, Zou Y, Wang Y, Lei JL, Zhao XN, Zeng X, Yan GJ. The relationship between processing speed and remodeling spatial patterns of intrinsic brain activity in the elderly with different sleep duration. Front Neurosci 2023; 17:1185078. [PMID: 37304029 PMCID: PMC10250673 DOI: 10.3389/fnins.2023.1185078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 04/26/2023] [Indexed: 06/13/2023] Open
Abstract
Objective Brain neuroplasticity in which sleep affects the speed of information processing in the elderly population has not been reported. Therefore, this study was conducted to explore the effects of sleep on information processing speed and its central plasticity mechanism in the elderly. Methods A total of 50 individuals aged 60 and older were enrolled in this case control study. All subjects were divided into two groups according to the sleep time: short sleep duration (< 360 min) (6 men and 19 women; mean age: 66.96 ± 4.28 years old), and non-short sleep duration (> 360 min) (13 men and 12 women). Resting-state functional magnetic resonance imaging (rs-fMRI) data were collected, and the amplitude of low frequency fluctuation (ALFF), regional homogeneity (ReHo), and degree centrality (DC) were calculated for each participant. Two-sample t-tests were performed to compare the ALFF, ReHo, and DC maps between the two groups. Then, the relationships among clinical features, fMRI and cognitive function were analyzed using general linear model. Results Short sleep duration group showed significantly increased ALFF value in the bilateral middle frontal gyrus and right insula; significantly increased ReHo value in the left superior parietal gyrus, and decreased ReHo value in the right crebellum; significantly decreased DC value in the left inferior occipital gyrus, left superior parietal gyrus and right cerebellum (p < 0.05, AlphaSim correction). The ALFF value of right insula is significantly associated with symbol digit modalities test (SDMT) score (β = -0.363, p = 0.033). Conclusion Short sleep duration and processing speed are significantly associated with remodeling spatial patterns of intrinsic brain activity in the elderly.
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Affiliation(s)
- Li Pu
- The Fourth People’s Hospital of Chengdu, Chengdu, China
| | - Yao Zou
- The Fourth People’s Hospital of Chengdu, Chengdu, China
| | - Yan Wang
- The Fourth People’s Hospital of Chengdu, Chengdu, China
| | - Jia-Ling Lei
- The Fourth People’s Hospital of Chengdu, Chengdu, China
| | - Xiao-Nan Zhao
- The Fourth People’s Hospital of Chengdu, Chengdu, China
| | - Xia Zeng
- Department of Neurology, Chengdu 363 Hospital, Chengdu, China
| | - Guo-Jian Yan
- The Fourth People’s Hospital of Chengdu, Chengdu, China
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Pu L, Liu H, Liu D, Zhao F, Dai X, Chen J. Novel marker for diagnosis of supracardiac total anomalous pulmonary venous connection in first trimester. Ultrasound Obstet Gynecol 2023; 61:653-655. [PMID: 36349882 DOI: 10.1002/uog.26112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/13/2022] [Accepted: 10/18/2022] [Indexed: 05/04/2023]
Affiliation(s)
- L Pu
- Department of Ultrasonic Medicine, West China Second Hospital of Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - H Liu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
- Department of Pediatric Pulmonology and Immunology, West China Second Hospital of Sichuan University, Chengdu, Sichuan, China
- NHC Key Laboratory of Chronobiology (Sichuan University), Chengdu, Sichuan, China
| | - D Liu
- Department of Ultrasonic Medicine, West China Second Hospital of Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - F Zhao
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
- Department of Radiology, West China Second Hospital of Sichuan University, Chengdu, Sichuan, China
| | - X Dai
- Department of Ultrasonic Medicine, West China Second Hospital of Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - J Chen
- Department of Ultrasonic Medicine, West China Second Hospital of Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
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Yin Y, Liu S, Pu L, Luo J, Liu H, Wu W. Nintedanib prevents TGF-β2-induced epithelial-mesenchymal transition in retinal pigment epithelial cells. Biomed Pharmacother 2023; 161:114543. [PMID: 36933383 DOI: 10.1016/j.biopha.2023.114543] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/04/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
Epithelial-mesenchymal transition (EMT) of retinal pigment epithelial (RPE) cells is a key fibrosis pathogenesis in proliferative vitreoretinopathy (PVR). However, few medicines can prevent proliferative membranes and cell proliferation in the clinic. Nintedanib, a tyrosine kinase inhibitor, has been shown to prevent fibrosis and be anti-inflammatory in multiple organ fibrosis. In our study, 0.1, 1, 10 μM nintedanib was added to 20 ng/mL transforming growth factor beta 2 (TGF-β2)-induced EMT in ARPE-19 cells. Western blot and immunofluorescence assay showed that 1 μM nintedanib suppressed TGF-β2-induced E-cadherin expression decreased and Fibronectin, N-cadherin, Vimentin, and α-SMA expression increased. Quantitative real-time PCR results showed that 1 μM nintedanib decreased TGF-β2-induced increase in SNAI1, Vimentin, and Fibronectin expression and increased TGF-β2-induced decrease in E-cadherin expression. In addition, the CCK-8 assay, wound healing assay, and collagen gel contraction assay also showed that 1 μM nintedanib ameliorated TGF-β2-induced cell proliferation, migration, and contraction, respectively. These results suggested that nintedanib inhibits TGF-β2-induced EMT in ARPE-19 cells, which may be a potential pharmacological treatment for PVR.
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Affiliation(s)
- Yiwei Yin
- Department of Pharmacy, Third Xiangya Hospital, Central South University, Changsha, China; Department of Ophthalmology, Hunan Key Laboratory of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
| | - Shikun Liu
- Department of Pharmacy, Third Xiangya Hospital, Central South University, Changsha, China
| | - Li Pu
- Department of Ophthalmology, Hunan Key Laboratory of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
| | - Jing Luo
- Department of Ophthalmology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Hanhan Liu
- Department of Ophthalmology, Third Xiangya Hospital, Central South University, Changsha, China.
| | - Wenyi Wu
- Department of Ophthalmology, Hunan Key Laboratory of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China.
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Wu L, Pu L, Zhuang Z. miR-155-5p/FOXO3a promotes pulmonary fibrosis in rats by mediating NLRP3 inflammasome activation. Immunopharmacol Immunotoxicol 2023; 45:257-267. [PMID: 35997271 DOI: 10.1080/08923973.2022.2115923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
OBJECTIVE Pulmonary fibrosis (PF) is regarded as progressive lung disease. miR-155-5p depletion exerts anti-fibrotic effects in silicotic mice. This study explored the effect and possible mechanism of miR-155-5p in PF rats, hoping to find a new target for PF management. METHODS Bleomycin-induced PF rat model was established. Alveolar structure and collagen fiber deposition were observed by HE and Elastica-Masson staining. Alveolitis and PF scores were evaluated using the method of Szapiel. Total collagen content was detected using the Sircol method. PF rats were intraperitoneally injected with NLRP3 inhibitor MCC950 or intravenously injected with miR-155-5p antagomir and si-FOXO3a lentivirus plasmids. Binding sites of miR-155-5p and FOXO3a were predicted using bioinformatics analysis and dual-luciferase reporter assay. The expressions of miR-155-5p, NLRP3, ASC, caspase-1, IL-1β, IL-18, and FOXO3a were detected by RT-qPCR, Western blot, and ELISA. RESULTS MCC950 treatment inhibited NLRP3 inflammasome, alleviated alveolar hemorrhage and alveolitis, and reduced blue collagen fiber deposition, scores of alveolitis and PF, and levels of NLRP3, ASC, caspase-1, IL-1β, and IL-18 in PF rats. miR-155-5p was elevated in lung tissues of PF rats. Inhibition of miR-155-5p downregulated levels of NLRP3, ASC, caspase-1, IL-1β, and IL-18 in lung tissues of PF rats. miR-155-5p targeted FOXO3a. miR-155-5p inhibition and silencing FOXO3a exacerbated alveolitis and PF in rats and increased levels of NLRP3, ASC, caspase-1, IL-1β, and IL-18. CONCLUSIONS miR-155-5p aggravated alveolitis and promoted PF by targeting FOXO3a and prompting the activation of NLRP3 inflammasome and then inducing IL-1β and IL-18 release.
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Affiliation(s)
- Ling Wu
- Department of Respiratory, Wujin Hospital Affiliated with Jiangsu University, Jiangsu Province, Changzhou, PR China
| | - Li Pu
- Department of Respiratory, Wujin Hospital Affiliated with Jiangsu University, Jiangsu Province, Changzhou, PR China
| | - Zhifang Zhuang
- Department of Respiratory, Wujin Hospital Affiliated with Jiangsu University, Jiangsu Province, Changzhou, PR China
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Wang W, Guo W, Le L, Yu J, Wu Y, Li D, Wang Y, Wang H, Lu X, Qiao H, Gu X, Tian J, Zhang C, Pu L. Integration of high-throughput phenotyping, GWAS, and predictive models reveals the genetic architecture of plant height in maize. Mol Plant 2023; 16:354-373. [PMID: 36447436 DOI: 10.1016/j.molp.2022.11.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/05/2022] [Accepted: 11/27/2022] [Indexed: 06/16/2023]
Abstract
Plant height (PH) is an essential trait in maize (Zea mays) that is tightly associated with planting density, biomass, lodging resistance, and grain yield in the field. Dissecting the dynamics of maize plant architecture will be beneficial for ideotype-based maize breeding and prediction, as the genetic basis controlling PH in maize remains largely unknown. In this study, we developed an automated high-throughput phenotyping platform (HTP) to systematically and noninvasively quantify 77 image-based traits (i-traits) and 20 field traits (f-traits) for 228 maize inbred lines across all developmental stages. Time-resolved i-traits with novel digital phenotypes and complex correlations with agronomic traits were characterized to reveal the dynamics of maize growth. An i-trait-based genome-wide association study identified 4945 trait-associated SNPs, 2603 genetic loci, and 1974 corresponding candidate genes. We found that rapid growth of maize plants occurs mainly at two developmental stages, stage 2 (S2) to S3 and S5 to S6, accounting for the final PH indicators. By integrating the PH-association network with the transcriptome profiles of specific internodes, we revealed 13 hub genes that may play vital roles during rapid growth. The candidate genes and novel i-traits identified at multiple growth stages may be used as potential indicators for final PH in maize. One candidate gene, ZmVATE, was functionally validated and shown to regulate PH-related traits in maize using genetic mutation. Furthermore, machine learning was used to build predictive models for final PH based on i-traits, and their performance was assessed across developmental stages. Moderate, strong, and very strong correlations between predictions and experimental datasets were achieved from the early S4 (tenth-leaf) stage. Colletively, our study provides a valuable tool for dissecting the spatiotemporal formation of specific internodes and the genetic architecture of PH, as well as resources and predictive models that are useful for molecular design breeding and predicting maize varieties with ideal plant architectures.
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Affiliation(s)
- Weixuan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Weijun Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Liang Le
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jia Yu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yue Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dongwei Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yifan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoduo Lu
- Institute of Molecular Breeding for Maize, Qilu Normal University, Jinan 250200, China
| | - Hong Qiao
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jian Tian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya 572000, China.
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China.
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Gai P, Pu L, Wang C, Zhu D, Li F. CeO2@NC nanozyme with robust dephosphorylation ability of phosphotriester: A simple colorimetric assay for rapid and selective detection of paraoxon. Biosens Bioelectron 2023; 220:114841. [DOI: 10.1016/j.bios.2022.114841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/23/2022] [Accepted: 10/19/2022] [Indexed: 11/29/2022]
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Wang Y, Tang Q, Pu L, Zhang H, Li X. CRISPR-Cas technology opens a new era for the creation of novel maize germplasms. Front Plant Sci 2022; 13:1049803. [PMID: 36589095 PMCID: PMC9800880 DOI: 10.3389/fpls.2022.1049803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Maize (Zea mays) is one of the most important food crops in the world with the greatest global production, and contributes to satiating the demands for human food, animal feed, and biofuels. With population growth and deteriorating environment, efficient and innovative breeding strategies to develop maize varieties with high yield and stress resistance are urgently needed to augment global food security and sustainable agriculture. CRISPR-Cas-mediated genome-editing technology (clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated)) has emerged as an effective and powerful tool for plant science and crop improvement, and is likely to accelerate crop breeding in ways dissimilar to crossbreeding and transgenic technologies. In this review, we summarize the current applications and prospects of CRISPR-Cas technology in maize gene-function studies and the generation of new germplasm for increased yield, specialty corns, plant architecture, stress response, haploid induction, and male sterility. Optimization of gene editing and genetic transformation systems for maize is also briefly reviewed. Lastly, the challenges and new opportunities that arise with the use of the CRISPR-Cas technology for maize genetic improvement are discussed.
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Affiliation(s)
- Youhua Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiaoling Tang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haiwen Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinhai Li
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
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Le L, Guo W, Du D, Zhang X, Wang W, Yu J, Wang H, Qiao H, Zhang C, Pu L. A spatiotemporal transcriptomic network dynamically modulates stalk development in maize. Plant Biotechnol J 2022; 20:2313-2331. [PMID: 36070002 PMCID: PMC9674325 DOI: 10.1111/pbi.13909] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/19/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Maize (Zea mays) is an important cereal crop with suitable stalk formation which is beneficial for acquiring an ideal agronomic trait to resist lodging and higher planting density. The elongation pattern of stalks arises from the variable growth of individual internodes driven by cell division and cell expansion comprising the maize stalk. However, the spatiotemporal dynamics and regulatory network of the maize stalk development and differentiation process remain unclear. Here, we report spatiotemporally resolved transcriptomes using all internodes of the whole stalks from developing maize at the elongation and maturation stages. We identified four distinct groups corresponding to four developmental zones and nine specific clusters with diverse spatiotemporal expression patterns among individual internodes of the stalk. Through weighted gene coexpression network analysis, we constructed transcriptional regulatory networks at a fine spatiotemporal resolution and uncovered key modules and candidate genes involved in internode maintenance, elongation, and division that determine stalk length and thickness in maize. Further CRISPR/Cas9-mediated knockout validated the function of a cytochrome P450 gene, ZmD1, in the regulation of stalk length and thickness as predicted by the WGCN. Collectively, these results provide insights into the high genetic complexity of stalk development and the potentially valuable resources with ideal stalk lengths and widths for genetic improvements in maize.
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Affiliation(s)
- Liang Le
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
- National Nanfan Research Institute (Sanya)Chinese Academy of Agricultural SciencesSanyaChina
| | - Weijun Guo
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Danyao Du
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Xiaoyuan Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Weixuan Wang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Jia Yu
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Huan Wang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Hong Qiao
- Institute for Cellular and Molecular Biology, The University of Texas at AustinAustinTXUSA
- Department of Molecular BiosciencesThe University of Texas at AustinAustinTXUSA
| | - Chunyi Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
- Sanya InstituteHainan Academy of Agricultural SciencesSanyaChina
| | - Li Pu
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
- National Nanfan Research Institute (Sanya)Chinese Academy of Agricultural SciencesSanyaChina
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Zhang D, Guo W, Wang T, Wang Y, Le L, Xu F, Wu Y, Wuriyanghan H, Sung ZR, Pu L. RNA 5-Methylcytosine Modification Regulates Vegetative Development Associated with H3K27 Trimethylation in Arabidopsis. Adv Sci (Weinh) 2022; 10:e2204885. [PMID: 36382558 PMCID: PMC9811455 DOI: 10.1002/advs.202204885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Methylating RNA post-transcriptionally is emerging as a significant mechanism of gene regulation in eukaryotes. The crosstalk between RNA methylation and histone modification is critical for chromatin state and gene expression in mammals. However, it is not well understood mechanistically in plants. Here, the authors report a genome-wide correlation between RNA 5-cytosine methylation (m5 C) and histone 3 lysine27 trimethylation (H3K27me3) in Arabidopsis. The plant-specific Polycomb group (PcG) protein EMBRYONIC FLOWER1 (EMF1) plays dual roles as activators or repressors. Transcriptome-wide RNA m5 C profiling revealed that m5 C peaks are mostly enriched in chromatin regions that lacked H3K27me3 in both wild type and emf1 mutants. EMF1 repressed the expression of m5 C methyltransferase tRNA specific methyltransferase 4B (TRM4B) through H3K4me3, independent of PcG-mediated H3K27me3 mechanism. The 5-Cytosine methylation on targets is increased in emf1 mutants, thereby decreased the mRNA transcripts of photosynthesis and chloroplast genes. In addition, impairing EMF1 activity reduced H3K27me3 levels of PcG targets, such as starch genes, which are de-repressed in emf1 mutants. Both EMF1-mediated promotion and repression of gene activities via m5 C and H3K27me3 are required for normal vegetative growth. Collectively, t study reveals a previously undescribed epigenetic mechanism of RNA m5 C modifications and histone modifications to regulate gene expression in eukaryotes.
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Affiliation(s)
- Daolei Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081P. R. China
- School of Life ScienceInner Mongolia UniversityHohhot010021P. R. China
| | - Weijun Guo
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081P. R. China
| | - Ting Wang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081P. R. China
- Shangrao Normal UniversityShangrao334001P. R. China
| | - Yifan Wang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081P. R. China
| | - Liang Le
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081P. R. China
| | - Fan Xu
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081P. R. China
| | - Yue Wu
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081P. R. China
| | - Hada Wuriyanghan
- School of Life ScienceInner Mongolia UniversityHohhot010021P. R. China
| | - Zinmay Renee Sung
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCA94720USA
| | - Li Pu
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081P. R. China
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Liu Z, Liu H, Zheng L, Xu F, Wu Y, Pu L, Zhang G. Enolase2 regulates seed fatty acid accumulation via mediating carbon partitioning in Arabidopsis thaliana. Physiol Plant 2022; 174:e13797. [PMID: 36251672 DOI: 10.1111/ppl.13797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/21/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
In many higher plants, fatty acid (FA) biosynthesis is coordinately regulated at multiple levels by intricate regulatory networks. However, the factors and their regulatory mechanisms underlying seed oil accumulation are still limited. Here, we identified that loss of glycolytic metalloenzyme enolase2 (AtENO2) activity increased the contents of total FAs and salicylic acid (SA) but reduced the accumulation of flavonoids and mucilage by regulating the expression of key genes involved in their biosynthesis pathway in Arabidopsis thaliana seeds. AtENO2 physically interacts with the transcription factor AtTGA5, which may participate in the regulation of SA levels. Non-targeted metabolomics analysis of eno2- and WT also showed that the levels of three flavonoids, quercetin-3-galactoside, quercitrin, and epicatechin, were significantly decreased in eno2- , and the flavonoid biosynthesis pathway was also enriched in the KEGG analysis. Meanwhile, the mutation of AtENO2 delayed silique ripening, thereby prolonging silique photosynthesis time, allowing siliques to generate more photosynthesis products for FA biosynthesis. These results reveal a molecular mechanism by AtENO2 to regulate seed oil accumulation in A. thaliana, providing potential targets for improving crop seed oil quality.
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Affiliation(s)
- Zijin Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Huimin Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Lamei Zheng
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Fan Xu
- Biotechnology Research Institute, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Yu Wu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Genfa Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
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Yang L, Zhang P, Wang Y, Hu G, Guo W, Gu X, Pu L. Plant synthetic epigenomic engineering for crop improvement. Sci China Life Sci 2022; 65:2191-2204. [PMID: 35851940 DOI: 10.1007/s11427-021-2131-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Efforts have been directed to redesign crops with increased yield, stress adaptability, and nutritional value through synthetic biology-the application of engineering principles to biology. A recent expansion in our understanding of how epigenetic mechanisms regulate plant development and stress responses has unveiled a new set of resources that can be harnessed to develop improved crops, thus heralding the promise of "synthetic epigenetics." In this review, we summarize the latest advances in epigenetic regulation and highlight how innovative sequencing techniques, epigenetic editing, and deep learning-driven predictive tools can rapidly extend these insights. We also proposed the future directions of synthetic epigenetics for the development of engineered smart crops that can actively monitor and respond to internal and external cues throughout their life cycles.
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Affiliation(s)
- Liwen Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Pingxian Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yifan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guihua Hu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Weijun Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Wu W, Pu L, Zhang E, Xiong S, Zhou X, Xia X, Wen D. Application of team-based learning to ophthalmology in China. Front Public Health 2022; 10:922325. [PMID: 36299748 PMCID: PMC9589088 DOI: 10.3389/fpubh.2022.922325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 06/22/2022] [Indexed: 01/22/2023] Open
Abstract
Objectives The purpose of this study was to explore whether team-based learning (TBL) was more effective than traditional didactic lectures (TDLs) in improving medical students' problem-solving and study skills in the clinical course of ophthalmology. In addition, we were also concerned about Chinese students' satisfaction with TBL. Methods Our study program involved 275 students of the 5-year clinical medicine program from Central South China University, of which 140 were enrolled in a modified TBL course. A questionnaire that included closed-ended and open-ended items was distributed to students immediately following the completion of the TBL session, and 108 valid questionnaires were collected. Descriptive statistics were used to analyze quantitative data. The effects of the TBL module on students' performance were measured between the groups using a one-way between-group analysis of variance (ANOVA) test by the individual readiness assurance test (IRAT), the group readiness assurance test (GRAT), and final examination scores (FESs), compared with a class without the TBL session. Results With our modified TBL strategy, 140 students achieved a mean test score of 72.65 on test questions that assessed their knowledge of ophthalmology compared to 135 students who achieved a mean score of 70.8 using the TDL method (p = 0.3434). The performance in a pre-class quiz was significantly better in the GRAT compared to the IRAT. In comparison to the TDL session, the modified TBL was preferred and acceptable by most medical students. Conclusions By applying the modified TBL to ophthalmology, students improved their performance, self-study, and teamwork, and their class engagement and satisfaction were enhanced. However, TBL should be further optimized and developed to enhance educational outcomes.
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Affiliation(s)
- Wenyi Wu
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China,Hunan Key Laboratory of Ophthalmology, Changsha, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Li Pu
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China,Hunan Key Laboratory of Ophthalmology, Changsha, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Endong Zhang
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China,Hunan Key Laboratory of Ophthalmology, Changsha, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Siqi Xiong
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China,Hunan Key Laboratory of Ophthalmology, Changsha, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaolai Zhou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaobo Xia
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China,Hunan Key Laboratory of Ophthalmology, Changsha, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Dan Wen
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China,Hunan Key Laboratory of Ophthalmology, Changsha, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China,*Correspondence: Dan Wen
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Yu X, Pu L, Xu Z, Yu T, Sun H. Regarding "The Role of Minimally Invasive Surgery in the Care of Women with Ovarian Cancer: A Systematic Review and Meta-analysis". J Minim Invasive Gynecol 2022; 29:1197. [DOI: 10.1016/j.jmig.2022.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 07/18/2022] [Indexed: 10/16/2022]
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ZHAN Y, He X, Pu L, Zou Y, He Q, Hong D, Li G. POS-197 INVESTIGATION ON THE ACHIEVEMENT OF CKD-MBD SERUM INDICATORS OF HEMODIALYSIS PATIENTS IN SICHUAN PROVINCE. Kidney Int Rep 2022. [DOI: 10.1016/j.ekir.2022.01.215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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ZHAN Y, He X, Pu L, Zhang Y, He Q, Hong D, Li G. POS-627 INVESTIGATION ON THE SEASONAL DISTRIBUTION OF HYPERKALEMIA IN HEMODIALYSIS PATIENT. Kidney Int Rep 2022. [DOI: 10.1016/j.ekir.2022.01.660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Zhu D, Zhang M, Pu L, Gai P, Li F. Nitrogen-Enriched Conjugated Polymer Enabled Metal-Free Carbon Nanozymes with Efficient Oxidase-Like Activity. Small 2022; 18:e2104993. [PMID: 34837456 DOI: 10.1002/smll.202104993] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/25/2021] [Indexed: 06/13/2023]
Abstract
Metal-free carbon nanozymes could be promising with the unique features of intrinsic catalytic ability, structure diversity, and strong tolerance to acidic/alkaline media. However, to date, the study of metal-free carbon nanozymes fell far behind metal-based nanomaterials, in which, the majority reported much more peroxidase-like activity than other enzyme-mimicking behavior (e.g., oxidase). Thus, the exploit of high-performance carbon nanozymes is of importance but challenging. In this work, the nitrogen-rich conjugated polymer (Aza-CPs) with rigid network structure is utilized as precursor to yield N-doped carbon material QAU-Z1 in high yield via a direct pyrolysis method. Surprisingly, QAU-Z1 stood out in oxidase-like behavior, which significantly outperformed the control materials GNC-900 and QAU-Z2 with nucleobase or conjugated small molecule as precursor, respectively. More importantly, it is a crucial revelation that the catalytic performance is closely related to the change of zeta potential for carbon nanozyme during the substrate 3,3',5,5'-tetramethylbenzidine oxidation process, as well as its catalytical capacity to O2 , which could be insightful to understand the inherent mechanism. This work not only presents the potential of conjugated polymers in constructing highly efficient carbon nanozyme, but also reveals the vital role of interaction mode between the nanozyme and substrate in the catalytic performance.
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Affiliation(s)
- Dangqiang Zhu
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, 266109, P. R. China
| | - Mengli Zhang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, 266109, P. R. China
| | - Li Pu
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, 266109, P. R. China
| | - Panpan Gai
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, 266109, P. R. China
| | - Feng Li
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, 266109, P. R. China
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He L, Li Y, Liao X, Wang Y, Pu L, Gao F, Wang G. Effects of evidence-based nursing combined with enhanced recovery after surgery on shoulder joint function and neurological function after arthroscopic rotator cuff injury repair. Medicine (Baltimore) 2021; 100:e27951. [PMID: 34964778 PMCID: PMC8615422 DOI: 10.1097/md.0000000000027951] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 11/02/2021] [Indexed: 01/05/2023] Open
Abstract
To explore the effect of Enhanced Recovery After Surgery (ERAS) nursing combined with limbs training on shoulder joint range of motion and neurological function of patients with rotator cuff injury after surgery.60 patients who underwent arthroscopic rotator cuff repair were randomly divided into experimental group and control group, with 30 cases in each group. The experimental group received ERAS nursing combined with rehabilitation training, while the control group received routine nursing. The prognostic effects of nursing care and shoulder joint range of motion between the two groups were compared.There were differences in general indicators between the two groups (P = .001). There was no significant difference in the evaluation indexes of the two groups of patients (P > .05). The visual analog scale score and the degree of swelling of the affected limb of the experimental group were lower than those of the control group (P = .001; .001). After 1, 6, 12 weeks of treatment, the Constant-Murley, American Shoulder and Elbow Surgeons and University of California-Los Angeles scores of the experimental group were higher than those of the control group (P = .001; .001; .001). After 2, 4 weeks of treatment, the National Institutes of Health Stroke Scale scores of the experimental group were lower than those of the control group (P = .001). The self-efficacy evaluation of the experimental group was significantly better than that of the control group (P = .001); the complication rate was lower than that of the control group (P = .006).Compared with simple postoperative nursing recovery, ERAS nursing combined with limbs training can improve the exercise capacity of the shoulder joint and the recovery of neurological function, reduce the occurrence of complications.
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Yan G, Pu L, Cui R, Gong D, Ma W, Yao D. Factors Related to Social Disturbance Among Patients With Mental Disorders Caused by Amphetamine-Type Stimulants. Int J Psychophysiol 2021. [DOI: 10.1016/j.ijpsycho.2021.07.546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Song X, Yan G, Pu L, Song M, Gong D, Ma W, Yao D. Characteristics of Attention Bias in Patients With Depression Disorder, and the Influence of High Frequency Transcranial Magnetic Stimulation Therapy on the Attention Bias. Int J Psychophysiol 2021. [DOI: 10.1016/j.ijpsycho.2021.07.556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Wang Y, Zhang P, Guo W, Liu H, Li X, Zhang Q, Du Z, Hu G, Han X, Pu L, Tian J, Gu X. A deep learning approach to automate whole-genome prediction of diverse epigenomic modifications in plants. New Phytol 2021; 232:880-897. [PMID: 34287908 DOI: 10.1111/nph.17630] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Epigenetic modifications function in gene transcription, RNA metabolism, and other biological processes. However, multiple factors currently limit the scientific utility of epigenomic datasets generated for plants. Here, using deep-learning approaches, we developed a Smart Model for Epigenetics in Plants (SMEP) to predict six types of epigenomic modifications: DNA 5-methylcytosine (5mC) and N6-methyladenosine (6mA) methylation, RNA N6-methyladenosine (m6 A) methylation, and three types of histone modification. Using the datasets from the japonica rice Nipponbare, SMEP achieved 95% prediction accuracy for 6mA, and also achieved around 80% for 5mC, m6 A, and the three types of histone modification based on the 10-fold cross-validation. Additionally, > 95% of the 6mA peaks detected after a heat-shock treatment were predicted. We also successfully applied the SMEP for examining epigenomic modifications in indica rice 93-11 and even the B73 maize line. Taken together, we show that the deep-learning-enabled SMEP can reliably mine epigenomic datasets from diverse plants to yield actionable insights about epigenomic sites. Thus, our work opens new avenues for the application of predictive tools to facilitate functional research, and will almost certainly increase the efficiency of genome engineering efforts.
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Affiliation(s)
- Yifan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Pingxian Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Weijun Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hanqing Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiulan Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qian Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhuoying Du
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guihua Hu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiao Han
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, China
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jian Tian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Kong X, Wang C, Pu L, Gai P, Li F. Self-Photocatalysis Boosted Electrochemiluminescence Signal Amplification via In Situ Generation of the Coreactant. Anal Chem 2021; 93:12441-12446. [PMID: 34464093 DOI: 10.1021/acs.analchem.1c02605] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The classic luminol-based electrochemiluminescence (ECL) platform generally suffers from self-decomposition of the coreactant (i.e., H2O2) during the reaction process, seriously hampering the luminous signal stability, as well as its practical application. To address this issue, apart from the introduction of complex exogenous species, preoxidation of the luminophore, and electrocatalysis for ECL signal amplification, we proposed a novel ECL model to realize the signal enhancement via in situ self-photocatalytic generation of the coreactant H2O2. Interestingly, the luminescence of luminol was simultaneously utilized as the light source to promote the conversation of O2 to H2O2 with the assistance of the photocatalyst resorcinol-formaldehyde resin, which could further improve the luminescence of luminol in turn. In comparison with the traditional case, this new ECL model not only exhibited obvious signal amplification but also efficiently boosted its stability of signal output. To sum up, an exogenous coreactant-free, highly stable ECL platform was obtained via simply integrating the photocatalyst RF and the luminol-based system. This work will not only inspire the design of a new integrated ECL system with a coreactant translator but also provide an ingenious insight for the construction of a new generation of ECL models.
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Affiliation(s)
- Xinke Kong
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Cui Wang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Li Pu
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Panpan Gai
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Feng Li
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, P. R. China
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Abstract
Electrochemiluminescence (ECL) is one powerful tool in the sensing field, in which the electrochemical workstation is necessary to achieve the electrical/optical signal conversion in the presence of luminescent agents. By contrast, biofuel cells (BFCs) can also provide electricity from renewable biofuels under moderate conditions. More importantly, BFCs with the features of adjustable voltage output and excellent compatibility would well meet the requirement of working voltages for different ECL devices. However, to the best of our knowledge, the BFC-driven luminous system has not been reported. In this work, we constructed, for the first time, a BFC-driven ECL system with fast and stable signal outputs. To demonstrate the proof-of-concept of the BFC-ECL system, the sensitive and selective detection of histidine was achieved, exhibiting great potential among point-of-care diagnoses in remote regions. Overall, this work not only paves a new way for the conversion of chemical energy, electrical energy, and luminous system but also explores the new application of BFC.
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Affiliation(s)
- Panpan Gai
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Xinke Kong
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Li Pu
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Mengli Zhang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Dangqiang Zhu
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Feng Li
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, P. R. China
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Yu R, Zuo T, Diao P, Fu J, Fan Y, Wang Y, Zhao Q, Ma X, Lu W, Li A, Wang R, Yan F, Pu L, Niu Y, Wuriyanghan H. Melatonin Enhances Seed Germination and Seedling Growth of Medicago sativa Under Salinity via a Putative Melatonin Receptor MsPMTR1. Front Plant Sci 2021; 12:702875. [PMID: 34490006 PMCID: PMC8418131 DOI: 10.3389/fpls.2021.702875] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/21/2021] [Indexed: 05/26/2023]
Abstract
Alfalfa (Medicago sativa L.) is an important forage crop, and salt stress is a major limiting factor in its yield. Melatonin (MT) is a multi-regulatory molecule in plants. We showed that basal MT content was positively correlated with the salt tolerance degree of different alfalfa varieties. MT and its precursor 5-HT fully recovered seed germination while partially ameliorated seedling growth of salt-stressed alfalfa. The 5-HT showed some divergent effects from MT with regards to growth amelioration under salinity. Salt stress caused stunted plant growth in soil culture, while MT ameliorated it by elevating plant height, fresh weight, branching number, and chlorophyll content. Silencing of a putative MT receptor, MsPMTR1, which was shown to be membrane-localized, abolished the ameliorative effects of MT on salt-stressed alfalfa seedling growth, while overexpression of MsPMTR1 improved plant growth under salt stress. The RNA sequencing analysis showed that nine pathway genes were specifically induced by MT treatment compared with salt stress. These MT-responsive differentially expressed genes include basal metabolic pathway genes, such as "ribosome, elongation factor," "sugar and lipid metabolism," and "photosynthesis" and stress-related genes encoding "membrane integrity" related proteins, heat shock protein, peroxidase/oxidoreductase, and protease. Several abiotic stress response-related genes, such as DRE, ARF, HD-ZF, MYB, and REM were repressed by NaCl treatment while induced by MT treatment. In summary, we demonstrated the importance of MsPMTR1 in MT-mediated salt tolerance in alfalfa, and we also analyzed the regulatory mechanism of MT during alfalfa seed germination under salt stress.
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Affiliation(s)
- Ruonan Yu
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Tiantian Zuo
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Pengfei Diao
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Jiabin Fu
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yanyan Fan
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China
- Department of Medicine, Ordos Institute of Technology, Ordos, China
| | - Yue Wang
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Qiqi Zhao
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Xuesong Ma
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Wenting Lu
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Aoga Li
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Ru Wang
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Fang Yan
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yiding Niu
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Hada Wuriyanghan
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China
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Pu L, Xia M, Sun P, Zhang Y. Ratiometric fluorescence determination of alkaline phosphatase activity based on dual emission of bovine serum albumin-stabilized gold nanoclusters and the inner filter effect. Analyst 2021; 146:943-948. [PMID: 33242047 DOI: 10.1039/d0an01978j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A novel and convenient method for the ratiometric fluorescence detection of alkaline phosphatase (ALP) activity was proposed based on dual emission of bovine serum albumin-templated gold nanoclusters (BSA-AuNCs) and the mechanism of the inner filter effect between BSA-AuNCs and p-nitrophenol (PNP). First, ALP catalyzed the hydrolysis of the substrate p-nitrophenyl phosphate (PNPP) to produce PNP. PNP effectively quenched the emission peak of BSA-AuNCs at 410 nm because of the overlap in absorbance feature of PNP and the fluorescence spectrum of BSA-AuNCs, and the peak at 650 nm was almost unaffected. Thus, a sensitive ratiometric method for detection of ALP activity was developed using the fluorescence intensity of BSA-AuNCs at 650 nm as a reference signal. ALP activity versus the ratio of fluorescence intensities at 410 and 650 nm showed good linearity between 0.2 and 5 mU mL-1 (R2 = 0.9931) and high sensitivity with a detection limit of 0.03 mU mL-1 (S/N = 3). The developed sensing method was successfully applied to investigate ALP inhibitors and detect ALP in serum samples.
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Affiliation(s)
- Li Pu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, China
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Long Q, Zhu W, Guo L, Pu L. RGD-Conjugated Resveratrol HSA Nanoparticles as a Novel Delivery System in Ovarian Cancer Therapy. Drug Des Devel Ther 2020; 14:5747-5756. [PMID: 33408463 PMCID: PMC7779302 DOI: 10.2147/dddt.s248950] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 08/12/2020] [Indexed: 11/23/2022]
Abstract
Background To establish a novel delivery system of RGD-conjugated resveratrol human serum albumin (HAS) nanoparticles in ovarian cancer therapy. Methods The nanoparticles system was characterized for physicochemical properties, the stability in the serum and in vitro release. The comparison between RVT injection, HSA-RVT NPs and RGD-HSA-RVT NPs regarding tissue distributions and pharmacokinetics was also carried out using mice as the animal models. Results The results showed that RGD-HSA-RVT NPs were characterized of small particle size about 128.2 nm and negative zeta potential about -21.42 mV, and drug controlled to release slowly on a biphasic pattern. Compared with control groups, RGD-HSA-RVT NPs showed the higher cellular uptake and cell inhibition rates. In vivo data showed that RGD-HSA-RVT NPs have good tumor enrichment characteristics and a significant difference in tumor inhibition, compared with the control group. Conclusion RGD-conjugated resveratrol HSA nanoparticles are an ideal drug delivery system, which can play a role in the treatment of ovarian cancer.
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Affiliation(s)
- Qifang Long
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
| | - Weipei Zhu
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
| | - Liangsheng Guo
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
| | - Li Pu
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
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Liu JY, Hua MX, Du CJ, Pu L, Xiang P, Li CS, Xiong HF, Liu XZ, Chen ZH, Xie W, Li A. The dual role of anti-viral therapy in the treatment of Coronavirus disease 2019. Eur Rev Med Pharmacol Sci 2020; 24:11939-11944. [PMID: 33275267 DOI: 10.26355/eurrev_202011_23854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OBJECTIVE Coronavirus disease 2019 (COVID-19) has become a worldwide public health emergency; unfortunately, there is currently no treatment for improving outcomes or reducing viral-clearance times in infected patients. The aim of the present study was to evaluate the efficacy of interferon (IFN) with or without lopinavir and ritonavir as antiviral therapeutic option for treating COVID-19 infection. PATIENTS AND METHODS The present study enrolled 148 patients that received either standard care, treatment with IFN alfa-2b, or IFN alfa-2b combined with lopinavir plus ritonavir. Viral testing was performed using Reverse-Transcription Polymerase Chain Reaction (RT-PCR). RESULTS There was no significant difference in the viral-clearance time at 28 days after treatment between patients receiving standard care and those receiving anti-viral treatments. However, the average viral-clearance time of patients receiving standard care (14 days) was shorter than that for patients receiving IFN alfa-2b or IFN alfa-2b combined with lopinavir plus ritonavir (15.5 or 17.5 days) (p<0.05). Patients treated with IFN alfa-2b within five days or IFN alfa-2b combined with lopinavir plus ritonavir after three days of symptoms exhibited shorter viral-clearance times than the other groups (p<0.05). Moreover, viral-clearance times were significantly longer in patients receiving standard care or anti-viral treatment 5 days after symptoms appeared than those of patients who received these treatments within five days of symptom onset (p<0.05). CONCLUSIONS Early symptomatic treatment is most critical for maximizing amelioration of COVID-19 infection. Anti-viral treatment might have complicated effect on viral-clearance.
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Affiliation(s)
- J-Y Liu
- Department of Intensive Care Unit, Beijing Ditan Hospital, Capital Medical University, Beijing, P. R. China.
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Yang X, Xiang Y, Wang F, Cai G, Li Y, Zhong L, Pu L, Yang Y, Song E. Expressions and relationship of Krüppel-like factor 15 and endothelial nitric oxide synthase in experimental deep venous thrombosis. Ann Transl Med 2020; 8:1090. [PMID: 33145309 PMCID: PMC7575959 DOI: 10.21037/atm-20-5828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Background Deep vein thrombosis (DVT) is an early postoperative complication. Thrombosis formation, which is potentially life-threatening, seriously affects the rehabilitation of patients after surgery. We aimed to establish a C57 mouse model of DVT and to examine the changes in the expression of Krüppel-like factor 15 (KLF15) and endothelial nitric oxide synthase (eNOS) in venous wall tissues, and we also investigated the regulatory relationship of KLF15 and eNOS in the thrombin-induced human umbilical vein endothelial cell (HUVEC) injury cell model. Methods The DVT model was established using the inferior vena cava (IVC) stenosis method. The expression levels of KLF15 and eNOS were analyzed using quantitative reverse transcription–polymerase chain reaction (qRT-PCR). In cell experiments, the expression of KLF15 and eNOS was analyzed in the model of thrombin-induced HUVEC injury with KLF15 siRNA. Results Compared to the control and sham-operated groups, KLF15 in the DVT group was upregulated, while eNOS was downregulated. The results of cell experiments revealed that KLF15 was downregulated in the thrombin+KLF15 siRNA group compared with the thrombin group. Meanwhile, eNOS was upregulated in the thrombin+KLF15 siRNA group compared with the thrombin group. These findings suggested that KLF15 regulated the expression of eNOS in the DVT model. Conclusions We successfully constructed a DVT mouse model. In the early stage of DVT formation, KLF15 regulated the expression and inhibited the antithrombotic effect of eNOS, resulting in thrombi formation.
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Affiliation(s)
- Xianguang Yang
- Department of Sports Medicine, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yaoyu Xiang
- Department of Sports Medicine, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Fuke Wang
- Department of Sports Medicine, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Guofeng Cai
- Department of Sports Medicine, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yanlin Li
- Department of Sports Medicine, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Ling Zhong
- Department of Sports Medicine, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Li Pu
- Department of Sports Medicine, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yang Yang
- Department of Sports Medicine, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - En Song
- Department of Sports Medicine, the First Affiliated Hospital of Kunming Medical University, Kunming, China
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36
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Xia X, Wu X, Zhou X, Zang Z, Pu L, Li Z. Comparison of Psychological Distress and Demand Induced by COVID-19 during the Lockdown Period in Patients Undergoing Peritoneal Dialysis and Hemodialysis: A Cross-Section Study in a Tertiary Hospital. Blood Purif 2020; 50:319-327. [PMID: 33113536 PMCID: PMC7705938 DOI: 10.1159/000510553] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/28/2020] [Indexed: 02/05/2023]
Abstract
Background Since the outbreak of COVID-19 in December 2019, it has spread rapidly and widely, bringing great psychological pressure to the public. In order to prevent the epidemic, traffic lockdown was required in many areas of China, which led to inconvenience of treatment for dialysis patients. This study was conducted to explore the psychological distress and the psychological demand induced by COVID-19 in the patients undergoing dialysis and compare the difference between hemodialysis (HD) and peritoneal dialysis (PD) patients during the traffic lockdown period. Methods Questionnaires were given to the dialysis patients in the West China Hospital of Sichuan University. The Impact of Event Scale (IES) was used to investigate the patients' trauma-related distress in response to COVID-19. Results 232 eligible respondents were enrolled in this cross-section study, consisting of 156 PD patients and 76 HD patients. The median IES score for all the enrolled patients was 8.00 (2.00–19.00), which belonged to the subclinical dimension of post-traumatic stress symptoms (PTSS). HD patients had a significant higher IES score than PD patients (11.50 vs. 8.00) (p < 0.05). HD patients already got more psychological support from the medical staff. According to IES scores, 22.4% HD patients and 13.4% PD patients were classified as having moderate or severe PTSS, which need psychological support (p < 0.05). But more patients of both groups considered psychological support was necessary (HD: 50%, PD: 45.5%) (p > 0.05). In the multivariate regression analysis, we found that dialysis vintage, the impact of COVID-19 on the severity of illness and daily life, and confidence in overcoming the disease contributed to IES score (p < 0.05). Conclusions HD patients had more severe trauma-related stress symptoms than PD patients. When major public healthy events occurred, careful psychological estimate and sufficient psychological support should be provided to the dialysis patients, especially to the HD patients.
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Affiliation(s)
- Xiaoxiao Xia
- Department of Nephrology, West China Hospital of Sichuan University, Chengdu, China.,West China School of Medicine, Sichuan University, Chengdu, China
| | - Xiaofang Wu
- Department of Nephrology, West China Hospital of Sichuan University, Chengdu, China.,West China School of Medicine, Sichuan University, Chengdu, China
| | - Xueli Zhou
- Department of Nephrology, West China Hospital of Sichuan University, Chengdu, China.,West China School of Nursing, West China Hospital of Sichuan University, Chengdu, China
| | - Zhiyun Zang
- Department of Nephrology, West China Hospital of Sichuan University, Chengdu, China.,West China School of Medicine, Sichuan University, Chengdu, China
| | - Li Pu
- Department of Nephrology, West China Hospital of Sichuan University, Chengdu, China.,West China School of Nursing, West China Hospital of Sichuan University, Chengdu, China
| | - Zi Li
- Department of Nephrology, West China Hospital of Sichuan University, Chengdu, China,
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Liu Z, Zheng L, Pu L, Ma X, Wang X, Wu Y, Ming H, Wang Q, Zhang G. ENO2 Affects the Seed Size and Weight by Adjusting Cytokinin Content and Forming ENO2-bZIP75 Complex in Arabidopsis thaliana. Front Plant Sci 2020; 11:574316. [PMID: 32983222 PMCID: PMC7479207 DOI: 10.3389/fpls.2020.574316] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/13/2020] [Indexed: 06/11/2023]
Abstract
Arabidopsis thaliana ENO2 (AtENO2) encodes two proteins AtENO2 (enolase) and AtMBP-1 (c-Myc binding protein 1-like). The loss of AtENO2 function causes the constitutive developmental defects which are correlated with reduced enolase activity, but not AtMBP-1 transcript abundance. However, the regulation mechanism of AtENO2 on the seed properties is still not clear. In this study, we found that the mutation of AtENO2 reduced the seed size and weight. The level of glucose in seed was significantly elevated but that of starch was decreased in AtENO2 mutants compared to WT plants. We also found that AtENO2 mutation reduced the content of cytokinin which resulted in smaller cotyledons. The RNA-seq data showed that there were 1892 differentially expressed genes and secondary metabolic pathways were significantly enriched. Instead of AtMBP-1, AtENO2 protein interacted with AtbZIP75 which may mediate the secondary metabolism. Therefore, ENO2 alters the size and weight of seeds which is not only regulated by the content of cytokinin and secondary metabolism, but may be affected by the interaction of ENO2 and bZIP57. These results are helpful to understand the novel function of AtENO2 which provide a foundation for further exploration of the key candidate genes for crop breeding.
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Affiliation(s)
- Zijin Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Lamei Zheng
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Xiaofeng Ma
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Xing Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yu Wu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Hainan Ming
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Qing Wang
- Institute of Radiation Botany, Beijing Radiation Center, Beijing, China
| | - Genfa Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
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38
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Yu J, Xu F, Wei Z, Zhang X, Chen T, Pu L. Epigenomic landscape and epigenetic regulation in maize. Theor Appl Genet 2020; 133:1467-1489. [PMID: 31965233 DOI: 10.1007/s00122-020-03549-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 01/14/2020] [Indexed: 05/12/2023]
Abstract
Epigenetic regulation has been implicated in the control of multiple agronomic traits in maize. Here, we review current advances in our understanding of epigenetic regulation, which has great potential for improving agronomic traits and the environmental adaptability of crops. Epigenetic regulation plays vital role in the control of complex agronomic traits. Epigenetic variation could contribute to phenotypic diversity and can be used to improve the quality and productivity of crops. Maize (Zea mays L.), one of the most widely cultivated crops for human food, animal feed, and ethanol biofuel, is a model plant for genetic studies. Recent advances in high-throughput sequencing technology have made possible the study of epigenetic regulation in maize on a genome-wide scale. In this review, we discuss recent epigenetic studies in maize many achieved by Chinese research groups. These studies have explored the roles of DNA methylation, posttranslational modifications of histones, chromatin remodeling, and noncoding RNAs in the regulation of gene expression in plant development and environment response. We also provide our future prospects for manipulating epigenetic regulation to improve crops.
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Affiliation(s)
- Jia Yu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ziwei Wei
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xiangxiang Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tao Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
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39
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Zhang X, Guo W, Du D, Pu L, Zhang C. Overexpression of a maize BR transcription factor ZmBZR1 in Arabidopsis enlarges organ and seed size of the transgenic plants. Plant Sci 2020; 292:110378. [PMID: 32005383 DOI: 10.1016/j.plantsci.2019.110378] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/26/2019] [Accepted: 12/10/2019] [Indexed: 05/18/2023]
Abstract
In plants, the organ size is one of the most important features and regulated by an elaborate developmental program involving both internal and external signals. The steroidal hormone brassinosteroid (BR) plays an important role in regulating the organ size. BRASSINAZOLE RESISTANT 1 (BZR1) is one of important transcription factors that regulate organ size in BR signal pathway in Arabidopsis. The function of BZR1 on organ size is well characterized in Arabidopsis, but poorly understood in maize (Zea mays). To understand the mechanism of intrinsic organ size regulated by BZR1 during organogenesis, we identified the maize BZR1 and examined its function in Arabidopsis. Overexpression of ZmBZR1 displayed phenotypes of enlarged cotyledons, rosette leaves, floral organ and seed size in Arabidopsis. The cells in rosette leaves as well as other organs in transgenic ZmBZR1 lines were dramatically larger and longer than those in Col-0. ChIP and RNA-seq analysis showed ZmBZR1 can directly bind to the promoter region of organ size related genes, Germination Repression and Cell Expansion receptor-like kinase (GRACE) and KIP-RELATED PROTEIN6 (KRP6) to regulate their expression, suggesting ZmBZR1 is required for the progressive increase in cells during Arabidopsis development. Collectively, our findings provide significant insights into the mechanisms underlying regulation of organ size mediated by maize BZR1.
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Affiliation(s)
- Xiaoyuan Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Weijun Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Danyao Du
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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40
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Wang D, Wang D, Pu L, Wei G. Improved Antioxidant Capacity and Immune Function of Broiler Chickens Fed with Selenium-enriched Candida utilis. Braz J Poult Sci 2020. [DOI: 10.1590/1806-9061-2019-1047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- D Wang
- Soochow University, China
| | - D Wang
- Soochow University, China
| | - L Pu
- Soochow University, China
| | - G Wei
- Soochow University, China
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Zhang R, Yin Y, Zhang S, Chen L, Pu L, Deng Q, Zhang H, Xiao L. Application of Differentially Methylated Loci in Clinical Diagnosis of Trisomy 21 Syndrome. Genet Test Mol Biomarkers 2019; 23:246-250. [PMID: 30986102 DOI: 10.1089/gtmb.2018.0176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
AIMS To determine the diagnostic precision of using different sets of fetal-specific methylation markers with methylation-sensitive restriction enzyme-quantitative polymerase chain reaction (MSRE-qPCR) for detection of trisomy 21 (T21). MATERIALS AND METHODS The diagnostic value for trisomy 21 of differential methylation of HLCS, C21orf25, and RASSF1A (a fetal-specific internal control) was examined by MSRE-qPCR. RESULTS The combined marker set of HLCS and RASSF1A achieved accurate quantification of fetal-specific chromosome 21 and was an excellent marker for detecting the presence of three copies of chromosome 21. MSRE-qPCR correctly identified three cases of fetal T21 from 11 clinical samples, which were 100% consistent with karyotyping results. In addition, this method was able to detect fetal-specific, T21-derived, cell-free fetal DNA at concentrations as low as 0.1%. CONCLUSIONS Evaluation of the HLCS and RASSF1A fetal-specific methylation marker set by MSRE-qPCR could be a highly sensitive, specific, cost-effective, and noninvasive prenatal screening method for T21. This MSRE-qPCR testable marker should be considered as an alternative to next generation sequencing technology for diagnosing fetal T21.
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Affiliation(s)
- Rong Zhang
- 1 Department of Obstetrics and Gynecology, Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yufang Yin
- 2 Department of Pharmacology and Neuroscience, School of Medicine, Southern Illinois University, Springfield, Illinois
| | - Shuyun Zhang
- 1 Department of Obstetrics and Gynecology, Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Li Chen
- 1 Department of Obstetrics and Gynecology, Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Li Pu
- 1 Department of Obstetrics and Gynecology, Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Qicheng Deng
- 1 Department of Obstetrics and Gynecology, Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Hong Zhang
- 1 Department of Obstetrics and Gynecology, Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Li Xiao
- 3 Department of Molecular Medicine Center, Second Affiliated Hospital of Soochow University, Suzhou, China
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Pu L, Su L, Kang X. The efficacy of cisplatin on nasopharyngeal carcinoma cells may be increased via the downregulation of fibroblast growth factor receptor 2. Int J Mol Med 2019; 44:57-66. [PMID: 31115494 PMCID: PMC6559331 DOI: 10.3892/ijmm.2019.4193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/12/2019] [Indexed: 11/06/2022] Open
Abstract
Cisplatin is one of the primary compounds used in the treatment of nasopharyngeal carcinoma (NPC), and fibroblast growth factor receptor 2 (FGFR2) has emerged to be a promising target for treatment in various tumors. Therefore, the present study aimed to explore whether the expression levels of FGFR2 in NPC tissues and cell lines were altered, and whether the efficiency of cisplatin was increased following the downregulation of FGFR2. The downregulation of FGFR2 was achieved by transfection with a small interfering RNA against FGFR2. Tissues of patients with NPC were analyzed by immunohistochemistry. Cell viability was examined using a Cell Counting Kit‑8 assay. Cell cycle analysis was performed using flow cytometry. mRNA and protein levels were measured by reverse transcription quantitative polymerase chain reaction and western blot analysis, respectively. FGFR2 was observed to be overexpressed in cancer tissues of patients with NPC and in the NPC SUNE1, C666‑1, 6‑10B and HNE‑3 cell lines, and resulted in an unfavorable prognosis. Cisplatin treatment decreased cell viability and increased FGFR2 expression. The silencing of FGFR2 was demonstrated to augment the effects of cisplatin treatment, including decreasing the cell viability and inducing cell cycle arrest, which involved the increase and decrease of the durations of G1 and S phases, respectively, and a decrease in the expression levels of cyclin D1 and CDC25A, and increasing the rate of apoptosis via the intrinsic apoptosis pathway, as demonstrated by the upregulation of cleaved caspase‑3 and B‑cell lymphoma 2 (Bcl‑2)‑associated X protein and downregulation of Bcl‑2, in SUNE1 and C666‑1 cell lines. FGFR2 was overexpressed in the cancer tissues of patients with NPC and in NPC cell lines, resulting in an unfavorable prognosis. The downregulation of FGFR2 decreased cell viability via cell cycle arrest at G1 phase, and increased the efficacy of the cisplatin‑based induction of apoptosis through the intrinsic apoptosis pathway.
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Affiliation(s)
- Li Pu
- Department of Otolaryngology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P.R. China
| | - Lizhong Su
- Department of Otolaryngology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P.R. China
| | - Xixun Kang
- Department of Otolaryngology, Head and Neck Surgery, Shenzhen Hospital, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518106, P.R. China
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Li C, Pu L, liu R, Shi B, Shia J. Evaluation of growth trend about nasal dorsum of patients influenced by cleft types. Int J Oral Maxillofac Surg 2019. [DOI: 10.1016/j.ijom.2019.03.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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44
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Sun L, Song G, Guo W, Wang W, Zhao H, Gao T, Lv Q, Yang X, Xu F, Dong Y, Pu L. Dynamic Changes in Genome-Wide Histone3 Lysine27 Trimethylation and Gene Expression of Soybean Roots in Response to Salt Stress. Front Plant Sci 2019; 10:1031. [PMID: 31552061 PMCID: PMC6746917 DOI: 10.3389/fpls.2019.01031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 07/23/2019] [Indexed: 05/14/2023]
Abstract
Soybean is an important economic crop for human diet, animal feeds and biodiesel due to high protein and oil content. Its productivity is significantly hampered by salt stress, which impairs plant growth and development by affecting gene expression, in part, through epigenetic modification of chromatin status. However, little is known about epigenetic regulation of stress response in soybean roots. Here, we used RNA-seq and ChIP-seq technologies to study the dynamics of genome-wide transcription and histone methylation patterns in soybean roots under salt stress. Eight thousand seven hundred ninety eight soybean genes changed their expression under salt stress treatment. Whole-genome ChIP-seq study of an epigenetic repressive mark, histone H3 lysine 27 trimethylation (H3K27me3), revealed the changes in H3K27me3 deposition during the response to salt stress. Unexpectedly, we found that most of the inactivation of genes under salt stress is strongly correlated with the de novo establishment of H3K27me3 in various parts of the promoter or coding regions where there is no H3K27me3 in control plants. In addition, the soybean histone modifiers were identified which may contribute to de novo histone methylation and gene silencing under salt stress. Thus, dynamic chromatin regulation, switch between active and inactive modes, occur at target loci in order to respond to salt stress in soybean. Our analysis demonstrates histone methylation modifications are correlated with the activation or inactivation of salt-inducible genes in soybean roots.
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Affiliation(s)
- Lei Sun
- College of Agriculture, Northeast Agricultural University, Harbin, China
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Guangshu Song
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Weijun Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weixuan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongkun Zhao
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Tingting Gao
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Qingxue Lv
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Xue Yang
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Fan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yingshan Dong
- College of Agriculture, Northeast Agricultural University, Harbin, China
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun, China
- *Correspondence: Yingshan Dong, ; Li Pu,
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Yingshan Dong, ; Li Pu,
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Cheng X, Zhang S, Tao W, Zhang X, Liu J, Sun J, Zhang H, Pu L, Huang R, Chen T. INDETERMINATE SPIKELET1 Recruits Histone Deacetylase and a Transcriptional Repression Complex to Regulate Rice Salt Tolerance. Plant Physiol 2018; 178:824-837. [PMID: 30061119 PMCID: PMC6181036 DOI: 10.1104/pp.18.00324] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/15/2018] [Indexed: 05/20/2023]
Abstract
Perception and transduction of salt stress signals are critical for plant survival, growth, and propagation. Thus, identification of components of the salt stress-signaling pathway is important for rice (Oryza sativa) molecular breeding of salt stress resistance. Here, we report the identification of an apetala2/ethylene response factor transcription factor INDETERMINATE SPIKELET1 (IDS1) and its roles in the regulation of rice salt tolerance. By genetic screening and phenotype analysis, we demonstrated that IDS1 conferred transcriptional repression activity and acted as a negative regulator of salt tolerance in rice. To identify potential downstream target genes regulated by IDS1, we conducted chromatin immunoprecipitation (ChIP) sequencing and ChIP-quantitative PCR assays and found that IDS1 may directly associate with the GCC-box-containing motifs in the promoter regions of abiotic stress-responsive genes, including LEA1 (LATE EMBRYOGENESIS ABUNDANT PROTEIN1) and SOS1 (SALT OVERLY SENSITIVE1), which are key genes regulating rice salt tolerance. IDS1 physically interacted with the transcriptional corepressor topless-related 1 and the histone deacetylase HDA1, contributing to the repression of LEA1 and SOS1 expression. Analyses of histone H3 acetylation status and RNA polymerase II occupation on the promoters of LEA1 and SOS1 further defined the molecular foundation of the transcriptional repression activity of IDS1. Our findings illustrate an epigenetic mechanism by which IDS1 modulates salt stress signaling as well as salt tolerance in rice.
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Affiliation(s)
- Xiliu Cheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, Beijing 100081,China
| | - Shaoxuan Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Weichun Tao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiangxiang Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jie Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, Beijing 100081,China
| | - Jiaqiang Sun
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, Beijing 100081,China
| | - Haiwen Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rongfeng Huang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tao Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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46
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Leng H, Pu L, Xu L, Shi X, Ji J, Chen K. Effects of aloe polysaccharide, a polysaccharide extracted from Aloe vera, on TNF‑α‑induced HaCaT cell proliferation and the underlying mechanism in psoriasis. Mol Med Rep 2018; 18:3537-3543. [PMID: 30066937 DOI: 10.3892/mmr.2018.9319] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 06/14/2018] [Indexed: 11/05/2022] Open
Abstract
Aloe vera is a traditional wound‑healing medicine used for the treatment of skin disorders. Aloe polysaccharide (APS) is the main macromolecule of Aloe vera, which contributes to its function. Psoriasis is an immune‑mediated chronic inflammatory disease, which affects 2‑3% of the general population. The conventional remedies used to treat psoriasis demonstrate limited effects; therefore, natural products, including Aloe vera, are being taken into consideration. However, the effects of APS on the treatment of psoriasis and the underlying mechanisms remain to be elucidated. The human keratinocyte cell line HaCaT was used to determine the effects of APS on psoriasis. Cells were randomly divided into five groups: i) Negative control group; ii) tumor necrosis factor (TNF)‑α stimulated psoriasis model group; and iii) APS (20, 40 and 80 µg/ml) pretreated psoriasis groups. Cell viability and proliferation were investigated using the CCK‑8 assay. ELISA and western blotting were applied to study the abundance of interleukin (IL)‑8 and IL‑12 in TNF‑α‑incubated culture medium and APS‑treated HaCaT cells, respectively. In addition, the mRNA expression levels of p65, and the protein expression levels of nuclear factor (NF)‑κB inhibitor‑α (IκBα) and phosphorylated‑p65, were detected by reverse transcription‑quantitative polymerase chain reaction and western blotting, respectively. APS was revealed to significantly reduce TNF‑α‑stimulated elevation of HaCaT cell proliferation in a dose‑dependent manner. The expression levels of inflammatory factors, including IL‑8 and IL‑12, were increased in response to TNF‑α. In addition, the mRNA and protein expression levels of p65 were increased following treatment with TNF‑α. Notably, treatment with APS was demonstrated to significantly attenuate the aforementioned effects in a dose‑dependent manner. Furthermore, IκBα protein expression levels were significantly reduced following treatment with TNF‑α, which was significantly reversed following treatment with APS. In conclusion, these results suggested that APS inhibited TNF‑α‑induced proliferation of keratinocytes and overactivation of the NF‑κB signaling pathway.
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Affiliation(s)
- Hong Leng
- Dermatological Department, Jiangsu Provincial Key Laboratory of Molecular Biology for Skin Disease and STIs, The Second Affiliated Hospital of Soochow University, Nanjing, Jiangsu 210042, P.R. China
| | - Li Pu
- Dermatological Department, Jiangsu Provincial Key Laboratory of Molecular Biology for Skin Disease and STIs, The Second Affiliated Hospital of Soochow University, Nanjing, Jiangsu 210042, P.R. China
| | - Longjiang Xu
- Dermatological Department, Jiangsu Provincial Key Laboratory of Molecular Biology for Skin Disease and STIs, The Second Affiliated Hospital of Soochow University, Nanjing, Jiangsu 210042, P.R. China
| | - Xin Shi
- Dermatological Department, Jiangsu Provincial Key Laboratory of Molecular Biology for Skin Disease and STIs, The Second Affiliated Hospital of Soochow University, Nanjing, Jiangsu 210042, P.R. China
| | - Jiang Ji
- Dermatological Department, Jiangsu Provincial Key Laboratory of Molecular Biology for Skin Disease and STIs, The Second Affiliated Hospital of Soochow University, Nanjing, Jiangsu 210042, P.R. China
| | - Kun Chen
- Dermatological Department, Jiangsu Provincial Key Laboratory of Molecular Biology for Skin Disease and STIs, The Second Affiliated Hospital of Soochow University, Nanjing, Jiangsu 210042, P.R. China
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Xu F, Kuo T, Rosli Y, Liu MS, Wu L, Chen LFO, Fletcher JC, Sung ZR, Pu L. Trithorax Group Proteins Act Together with a Polycomb Group Protein to Maintain Chromatin Integrity for Epigenetic Silencing during Seed Germination in Arabidopsis. Mol Plant 2018; 11:659-677. [PMID: 29428247 DOI: 10.1016/j.molp.2018.01.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 01/01/2018] [Accepted: 01/29/2018] [Indexed: 05/02/2023]
Abstract
Polycomb group (PcG) and trithorax group (trxG) proteins have been shown to act antagonistically to epigenetically regulate gene expression in eukaryotes. The trxG proteins counteract PcG-mediated floral repression in Arabidopsis, but their roles in other developmental processes are poorly understood. We investigated the interactions between the trxG genes, ARABIDOPSIS HOMOLOG OF TRITHORAX1 (ATX1) and ULTRAPETALA1 (ULT1), and the PcG gene EMBRYONIC FLOWER 1 (EMF1) during early development. Unexpectedly, we found that mutations in the trxG genes failed to rescue the early-flowering phenotype of emf1 mutants. Instead, emf1 atx1 ult1 seedlings showed a novel swollen root phenotype and massive deregulation of gene expression. Greater ectopic expression of seed master regulatory genes in emf1 atx1 ult1 triple than in emf1 single mutants indicates that PcG and trxG factors together repress seed gene expression after germination. Furthermore, we found that the widespread gene derepression is associated with reduced levels of H3K27me3, an epigenetic repressive mark of gene expression, and with globally altered chromatin organization. EMF1, ATX1, and ULT1 are able to bind the chromatin of seed genes and ULT1 can physically interact with ATX1 and EMF1, suggesting that the trxG and EMF1 proteins directly associate at target gene loci for EMF1-mediated gene silencing. Thus, while ATX1, ULT1, and EMF1 interact antagonistically to regulate flowering, they work together to maintain chromatin integrity and prevent precocious seed gene expression after germination.
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Affiliation(s)
- Fan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tony Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529 Taiwan, China
| | - Yenny Rosli
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Mao-Sen Liu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529 Taiwan, China
| | - Limin Wu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Long-Fang Oliver Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529 Taiwan, China
| | - Jennifer C Fletcher
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Zinmay Renee Sung
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
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48
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Yang H, Yang J, Han LD, Liu X, Pu L, Chin SM, Hwang HL. A Kriging based spatiotemporal approach for traffic volume data imputation. PLoS One 2018; 13:e0195957. [PMID: 29664928 PMCID: PMC5903649 DOI: 10.1371/journal.pone.0195957] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 04/03/2018] [Indexed: 12/05/2022] Open
Abstract
Along with the rapid development of Intelligent Transportation Systems, traffic data collection technologies have progressed fast. The emergence of innovative data collection technologies such as remote traffic microwave sensor, Bluetooth sensor, GPS-based floating car method, and automated license plate recognition, has significantly increased the variety and volume of traffic data. Despite the development of these technologies, the missing data issue is still a problem that poses great challenge for data based applications such as traffic forecasting, real-time incident detection, dynamic route guidance, and massive evacuation optimization. A thorough literature review suggests most current imputation models either focus on the temporal nature of the traffic data and fail to consider the spatial information of neighboring locations or assume the data follow a certain distribution. These two issues reduce the imputation accuracy and limit the use of the corresponding imputation methods respectively. As a result, this paper presents a Kriging based data imputation approach that is able to fully utilize the spatiotemporal correlation in the traffic data and that does not assume the data follow any distribution. A set of scenarios with different missing rates are used to evaluate the performance of the proposed method. The performance of the proposed method was compared with that of two other widely used methods, historical average and K-nearest neighborhood. Comparison results indicate that the proposed method has the highest imputation accuracy and is more flexible compared to other methods.
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Affiliation(s)
- Hongtai Yang
- National United Engineering Laboratory of Integrated and Intelligent Transportation, School of Transportation and Logistics, Southwest Jiaotong University, Hi-Tech Industrial Development Zone, Chengdu, Sichuan, China
| | - Jianjiang Yang
- Model Risk Management, Bank of America, Charlotte, NC, United States of America
| | - Lee D. Han
- Department of Civil & Environmental Engineering, the University of Tennessee, Knoxville, TN, United States of America
- * E-mail:
| | - Xiaohan Liu
- National United Engineering Laboratory of Integrated and Intelligent Transportation, School of Transportation and Logistics, Southwest Jiaotong University, Hi-Tech Industrial Development Zone, Chengdu, Sichuan, China
| | - Li Pu
- School of Architecture and Design, Southwest Jiaotong University, Hi-Tech Industrial Development Zone, Chengdu, Sichuan, China
| | - Shih-miao Chin
- Center for Transportation Analysis, Oak Ridge National Laboratory, Cherahala Boulevard, Knoxville, TN, United States of America
| | - Ho-ling Hwang
- Center for Transportation Analysis, Oak Ridge National Laboratory, Cherahala Boulevard, Knoxville, TN, United States of America
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Richter U, Kronburg MB, Huo Y, Sitzy J, Pu L, Mayer J, Ulbrich S, Gaspar T, Piorkowski C. P1214From trials to clinical practice: True outcome of AF landmark trials and studies. Europace 2018. [DOI: 10.1093/europace/euy015.696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- U Richter
- University Hospital Dresden, Electrophysiology, Dresden, Germany
| | - M B Kronburg
- Aarhus University Hospital, Electrophysiology, Aarhus, Denmark
| | - Y Huo
- University Hospital Dresden, Electrophysiology, Dresden, Germany
| | - J Sitzy
- University Hospital Dresden, Electrophysiology, Dresden, Germany
| | - L Pu
- University Hospital Dresden, Electrophysiology, Dresden, Germany
| | - J Mayer
- University Hospital Dresden, Electrophysiology, Dresden, Germany
| | - S Ulbrich
- University Hospital Dresden, Electrophysiology, Dresden, Germany
| | - T Gaspar
- University Hospital Dresden, Electrophysiology, Dresden, Germany
| | - C Piorkowski
- University Hospital Dresden, Electrophysiology, Dresden, Germany
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50
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Huo Y, Kronborg MB, Ulbrich S, Zedda A, Mayer J, Pu L, Guo J, Richter U, Sitzy J, Gaspar T, Piorkowski C. P364Presence of low voltage zone areas is associated with lower AF recurrence in patients undergoing re-ablation with substrate modification. Europace 2018. [DOI: 10.1093/europace/euy015.175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Y Huo
- Dresden University of Technology, Heart Center University Hospital, Dresden, Germany
| | - M B Kronborg
- Dresden University of Technology, Heart Center University Hospital, Dresden, Germany
| | - S Ulbrich
- Dresden University of Technology, Heart Center University Hospital, Dresden, Germany
| | - A Zedda
- Dresden University of Technology, Heart Center University Hospital, Dresden, Germany
| | - J Mayer
- Dresden University of Technology, Heart Center University Hospital, Dresden, Germany
| | - L Pu
- Dresden University of Technology, Heart Center University Hospital, Dresden, Germany
| | - J Guo
- Dresden University of Technology, Heart Center University Hospital, Dresden, Germany
| | - U Richter
- Dresden University of Technology, Heart Center University Hospital, Dresden, Germany
| | - J Sitzy
- Dresden University of Technology, Heart Center University Hospital, Dresden, Germany
| | - T Gaspar
- Dresden University of Technology, Heart Center University Hospital, Dresden, Germany
| | - C Piorkowski
- Dresden University of Technology, Heart Center University Hospital, Dresden, Germany
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