Publications by authors named "Bao Liu"

451 Publications

Analysis of expression characteristics of soybean leaf and root tissue-specific promoters in Arabidopsis and soybean.

Transgenic Res 2021 Jun 11. Epub 2021 Jun 11.

Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, 130033, Changchun, China.

The characterization of tissue-specific promoters is critical for studying the functions of genes in a given tissue/organ. To study tissue-specific promoters in soybean, we screened tissue-specific expressed genes using published soybean RNA-Seq-based transcriptome data coupled with RT-PCR analysis. We cloned the promoters of three genes, GmADR1, GmBTP1, and GmGER1, and constructed their corresponding β-Glucuronidase (GUS) promoter-GUS reporter vectors. We generated transgenic Arabidopsis plants and examined the expression patterns of these promoters by GUS staining and RT-PCR analysis. We also transformed the promoter-GUS reporter vectors into soybean to obtain hairy roots, and examined promoter expression by GUS staining. We found a root-specific expression pattern of GmADR1 and GmBTP1 in both Arabidopsis and soybean, and the promoter of GmGER1 showed a leaf-specific pattern in transgenic Arabidopsis plants. To test the potential utility of these promoters in soybean improvement by transgenic means, we used the GmADR1 promoter to drive expression of a salt resistance gene in soybean, GmCaM4, by generating transgenic soybean plants. We found that the transgenic plants had significantly enhanced salt tolerance compared to non-transformed wild-type, suggesting that introducing endogenous promoters by transgenic means can drive the expression of functional genes in specific tissues and organs in soybean.
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http://dx.doi.org/10.1007/s11248-021-00266-7DOI Listing
June 2021

Selecting Proper Region of Interest and Parameters Affects Feasibility of Two Dimensional Perfusion Angiography.

Authors:
Jiangyu Ma Bao Liu

Eur J Vasc Endovasc Surg 2021 Jun 7. Epub 2021 Jun 7.

Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, People's Republic of China. Electronic address:

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http://dx.doi.org/10.1016/j.ejvs.2021.05.005DOI Listing
June 2021

Genome-wide (ChIP-seq) identification of target genes regulated by WRKY33 during submergence stress in Arabidopsis.

BMC Genom Data 2021 05 24;22(1):16. Epub 2021 May 24.

Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, 610065, China.

Background: Hypoxia induced by flooding causes significant losses to crop production almost every year. However, the molecular network of submergence signaling pathway is still poorly understood. According to previous studies, transgenic plants overexpressing the WRKY33 gene showed enhanced resistance to submergence stress. Thus, this transcription factor may regulate a series of target genes in response to submergence. Here, to determine putative downstream targets of WRKY33 at a genome-wide scale in Arabidopsis thaliana, we performed the chromatin immunoprecipitation sequencing (ChIP-seq) using 35S:FLAG-WRKY33 overexpression transgenic lines (WRKY33-OE) after 24 h of submergence treatment.

Results: Using ChIP-seq data, we identified a total of 104 WRKY33-binding genes under submergence stress (WRKY33BGSs). Most WRKY33BGSs are involved in the oxidation-reduction process, programmed cell death in response to reactive oxygen species, lipid biosynthesis process, and other processes related to stress responses. Moreover, the major motif identified in the WRKY33BGSs promoters is a new cis-element, TCTCTC (named here as "TC box"). This cis-element differs from the previously known W box for WRKY33. Further qPCR experiments verified that genes carrying this motif in their promoters could be regulated by WRKY33 upon submergence treatment.

Conclusions: Our study has identified a new putative binding motif of WRKY33 and recovered numerous previously unknown target genes of WRKY33 during submergence stress. The WRKY33 gene positively participates in flooding response probably by transcriptional regulation of the downstream submergence-related target genes via a "TC box".
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http://dx.doi.org/10.1186/s12863-021-00972-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8142642PMC
May 2021

Ginsenoside Rh7 Suppresses Proliferation, Migration and Invasion of NSCLC Cells Through Targeting ILF3-AS1 Mediated miR-212/SMAD1 Axis.

Front Oncol 2021 29;11:656132. Epub 2021 Apr 29.

Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China.

It is reported that ginsenosides have a significant anti-tumor effect on a variety of tumors. However, the role and mechanism of Rh7 in non-small cell lung cancer (NSCLC) are unclear. In this study, we aimed to study the anti-tumor effect of Rh7 on the proliferation and progression of NSCLC. Bioinformatics analysis showed that ILF3-AS1 was regulated by ginsenoside Rh7 in NSCLC. Down-regulation of ILF3-AS1 could significantly inhibit the proliferation, metastasis and invasion of NSCLC. In addition, ILF3-AS1 negatively controlled miR-212, which in turn targeted SMAD1 expression, thereby regulating NSCLC cell viability and apoptosis. Our results indicate that ILF3-AS1 can be used as a diagnostic and therapeutic target for non-small cell lung cancer. It is discovered for the first time that ginsenoside Rh7 inhibits the expression of ILF3-AS1 and exerts antitumor effects.
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http://dx.doi.org/10.3389/fonc.2021.656132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8116958PMC
April 2021

[Latest Progresses in Surgical Treatment of Median Arcuate Ligament Syndrome].

Zhongguo Yi Xue Ke Xue Yuan Xue Bao 2021 Apr;43(2):283-287

Department of Vascular Surgery,PUMC Hospital,CAMS and PUMC,Beijing 100730,China.

Median arcuate ligament syndrome(MALS)is compression of the celiac trunk by the median arcuate ligament.Median arcuate ligament release is the corner stone for the surgical treatment of MALS.Open surgery,laparoscopic surgery,and robot-assisted surgery have been developed,among which laparoscopic surgery has been proposed as the preferred approach in view of its minimal trauma and short hospital stay.Auxiliary celiac plexus neurolysis could further alleviate the patient's discomfort.Moreover,vascular reconstitution is of vital importance in the case of persistent stenosis in the celiac artery despite of median arcuate ligament decompression.Vascular reconstruction has satisfactory long-term patency rate,while endovascular treatment is less invasive.This article aims to summarize the consensuses and advances and shed light on the surgical treatment of MALS.
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http://dx.doi.org/10.3881/j.issn.1000-503X.11980DOI Listing
April 2021

Prevalence and Risk Factors for Anxiety and Depression in Patients With COVID-19 in Wuhan, China.

Psychosom Med 2021 05;83(4):368-372

From the Surgery Intensive Care Unit (Li, Liu, Wang, Zhang, Gong, Duan) China-Japan Friendship Hospital; and Peking University Institute of Mental Health (Sun), National Clinical Research Center for Mental Disorders, Beijing, China.

Objective: Infectious diseases can cause psychological changes in patients. This study aimed to evaluate the prevalence and related risk factors for anxiety and depression in patients with COVID-19.

Methods: A cross-sectional study was performed on patients with COVID-19 admitted to the Sino-French New City branch of Wuhan Tongji Hospital from January to February 2020. The Zung Self-Rating Anxiety and Depression Scales were used to evaluate the prevalence of anxiety and depression. Demographic, clinical, and sociological data were also collected. Multivariable logistic regression analysis was used to identify independent risk factors of anxiety and depression in patients with COVID-19.

Results: In the current study, 183 patients were enrolled (mean age = 53 ± 9 years; 41.1% women). The prevalences of anxiety and depression were 56.3% and 39.3%, respectively. Logistic regression analysis revealed that older age, female sex, being divorced or widowed, COVID-19 disease duration, renal disease, and depression were identified as independent risk factors for anxiety in patients with COVID-19. Factors that were associated with depression were female sex, being widowed, COVID-19 disease duration, and anxiety.

Conclusions: This study demonstrates a high prevalence of anxiety and depression in patients with COVID-19 at the peak of the epidemic in Wuhan, China. The identification of demographic, clinical, and social factors may help identify health care professionals to provide psychological care as part of treatment for patients with COVID-19 and other life-threatening infectious diseases.
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http://dx.doi.org/10.1097/PSY.0000000000000934DOI Listing
May 2021

Enhanced field emission performance of MXene-TiO composite films.

Nanoscale 2021 Apr;13(16):7622-7629

Laboratory of Clean Energy Chemistry and Materials, State Key Laboratory of Solid Lubrication, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, China. and Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China.

A facile method to produce an MXene-TiO2 composite is demonstrated for enhanced field emission display applications. The field emission performance of two-dimensional free-standing and linear-shaped field emitters has been systematically investigated and enhanced electron emission behaviors (e.g. emission current, stability and emission patterns) are achieved by compositing MXene and TiO2 nanowires. The relationship between the emission current density, electric field and anode-cathode gap distance is studied and the emitters, especially the cross-section of the composite film, show good performance. The emission current from the cross-section of the composite film can reach 289 mA cm-2, which is the best result of the state of the art compared to single MXene and TiO2 nanowires. We have also reported a triboelectric nanogenerator powered by free-standing MXene-TiO2 composite emitters, implying the feasibility of the self-powering field emission devices and possibly enlarging the applications of cold emitters in various fields.
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http://dx.doi.org/10.1039/d0nr08900aDOI Listing
April 2021

Long non-coding RNA AFAP1-AS1 facilitates ovarian cancer progression by regulating the miR-107/PDK4 axis.

J Ovarian Res 2021 Apr 29;14(1):60. Epub 2021 Apr 29.

Chongqing Health Center for Women and Children, Chongqing, 401147, China.

Background: Abnormally expressed in various tumors, long non-coding RNAs (lncRNAs) feature prominently in tumor development, yet little is still known regarding the functional roles of lncRNA AFAP1 antisense RNA 1 (AFAP1-AS1) in ovarian cancer (OC).

Methods: The relative expression levels of lncRNA AFAP1-AS1, microRNA (miR)-107 and pyruvate dehydrogenase kinase isozyme 4 (PDK4) mRNA were assessed by quantitative real-time PCR. PDK4, PCNA and cyclin D1 expression levels were determined using Western blot analysis. Bioinformatics analysis and dual-luciferase gene reporter assay were conducted for identifying and validating the binding sequences between AFAP1-AS1 and miR-107, as well as between miR-107 and PDK4. Cell counting kit-8 assay was employed for detecting cell proliferation. Cell migration and invasion abilities were examined using Transwell assays.

Results: The present study revealed that AFAP1-AS1 expression was elevated in OC cells and tissues. AFAP1-AS1 expression and FIGO stage were positively correlated. AFAP1-AS1 knockdown repressed OC cell proliferation, migration and invasion. AFAP1-AS1 functioned as a sponge of miR-107, and miR-107 reversed the effects of AFAP1-AS1 on OC cells. It was validated that miR-107 was able to bind to PDK4, and AFAP1-AS1 regulated PDK4 expression by competitively binding with miR-107. Additionally, miR-107 modulated OC cell proliferation, migration and invasion via targeting PDK4.

Conclusions: LncRNA AFAP1-AS1 serves as a tumor driver in the pathogenesis of OC via the miR-107/PDK4 axis.
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http://dx.doi.org/10.1186/s13048-021-00808-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8086133PMC
April 2021

Homoploid F1 hybrids and segmental allotetraploids of rice subspecies are similarly more tolerant to N-deficiency than are parental lines.

J Exp Bot 2021 Apr 28. Epub 2021 Apr 28.

Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China.

Whether merger of two divergent genomes by hybridization at the homoploid level or coupled with WGD (allopolyploidy) can bestow plants better tolerance to stress conditions remains understudied. In this study, two diploid rice (Oryza sativa L.) subspecies, japonica, and indica, their reciprocal F1 hybrids and segmental allotetraploids were compared for phenotypic performance and gene expression under normal and nitrogen (N)-deficient conditions. We found that F1 hybrids and tetraploids showed higher tolerance at similar levels than did either parent. In parallel, total expression levels of 18 relevant functional genes were less perturbed by nitrogen deficiency in F1 hybrids and tetraploids than in the parents. This is consistent with stable intrinsic partitioning of allelic/homoeologous expression defined by parental legacy in the homoploid F1 hybrids/tetraploids between the two conditions. Our results suggest that genetic additivity at both the homoploid level or allopolyploidy may lead to similar beneficial phenotypic responses to nitrogen stress compared with their parents. The lack of synergistic responses to nitrogen limitation concomitant with WGD, relative to that exhibited by F1 hybrids, adds new empirical evidence in support of the emerging notion that hybridization by itself may play a significant role in plant adaptive evolution in times of stress.
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http://dx.doi.org/10.1093/jxb/erab184DOI Listing
April 2021

High Chromosomal Stability and Immortalized Totipotency Characterize Long-Term Tissue Cultures of Chinese Ginseng ().

Genes (Basel) 2021 Mar 31;12(4). Epub 2021 Mar 31.

Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China.

Chinese ginseng ( C. A. Meyer) is a highly cherished traditional Chinese medicine, with several confirmed medical effects and many more asserted health-boosting functions. Somatic chromosomal instability (CIN) is a hallmark of many types of human cancers and also related to other pathogenic conditions such as miscarriages and intellectual disabilities, hence, the study of this phenomenon is of wide scientific and translational medical significance. CIN also ubiquitously occurs in cultured plant cells, and is implicated as a major cause of the rapid decline/loss of totipotency with culture duration, which represents a major hindrance to the application of transgenic technologies in crop improvement. Here, we report two salient features of long-term cultured callus cells of ginseng, i.e., high chromosomal stability and virtually immortalized totipotency. Specifically, we document that our callus of ginseng, which has been subcultured for 12 consecutive years, remained highly stable at the chromosomal level and showed little decline in totipotency. We show that these remarkable features of cultured ginseng cells are likely relevant to the robust homeostasis of the transcriptional expression of specific genes (i.e., genes related to tissue totipotency and chromosomal stability) implicated in the manifestation of these two complex phenotypes. To our knowledge, these two properties of ginseng have not been observed in any animals (with respect to somatic chromosomal stability) and other plants. We posit that further exploration of the molecular mechanisms underlying these unique properties of ginseng, especially somatic chromosomal stability in protracted culture duration, may provide novel clues to the mechanistic understanding of the occurrence of CIN in human disease.
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http://dx.doi.org/10.3390/genes12040514DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8067114PMC
March 2021

Proposed modification to the Shamblin's classification of carotid body tumors: A single-center retrospective experience of 116 tumors.

Eur J Surg Oncol 2021 Mar 20. Epub 2021 Mar 20.

Department of Vascular Surgery, Peking Union Medical College Hospital, Shuaifuyuan 1, Dongcheng District, Beijing, 100730, China. Electronic address:

Objectives: Carotid body tumors (CBTs) are rare head and neck neoplasms, we aimed to propose a modification to the Shamblin's classification of CBTs.

Materials And Methods: This retrospective study included 105 patients (116 CBTs) operated at our institution from March 2013 to July 2020. CBTs were divided by a modified Shamblin's classification into five subtypes (type I-V) based on the radiographic features. Correlations between modified classification and intraoperative bleeding, internal carotid artery (ICA) bypass and postoperative neural complications, as main outcomes, as well as other outcomes were analyzed.

Results: Surgeries for type V and type I CBTs had the most (median: 700 ml, IQR: 375-1575 ml) and least (median: 20 ml, IQR: 20-50 ml) bleeding, respectively. Intraoperatively, ICA bypass was needed in 41.7% (10/24) type V, 18.2% (8/44) type IV and 5.9% (1/17) type III lesions, but not in other subtypes (p = .001). Postoperatively, overall cranial nerve deficits (CND) were found most frequently in type V tumors (17/24, 70.8%) (p = .016). Permanent CND were found in 33.3% (8/24) type V and 4.5% (2/44) type IV lesions, but not in other subtypes (p = .001). Other outcomes including external carotid artery ligation, operation time, blood transfusion, postoperative intensive unit care and postoperative hospitalization also showed significant difference among different subtypes. Patients recovered uneventfully during a follow-up of 23.5 ± 16.2 months except for one ipsilateral recurrence at 42 months after surgery.

Conclusions: The modified classification was correlated with surgical outcomes of CBTs and will be helpful for making surgical plans.
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http://dx.doi.org/10.1016/j.ejso.2021.03.244DOI Listing
March 2021

DL-3-n-butylphthalide improved physical and learning and memory performance of rodents exposed to acute and chronic hypobaric hypoxia.

Mil Med Res 2021 03 25;8(1):23. Epub 2021 Mar 25.

Institute of Medicine and Equipment for High Altitude Region, College of High Altitude Military Medicine, Army Medical University, Number 30, Gaotanyan Street, District of Shapingba, Chongqing, 400038, China.

Background: Studies have revealed the protective effect of DL-3-n-butylphthalide (NBP) against diseases associated with ischemic hypoxia. However, the role of NBP in animals with hypobaric hypoxia has not been elucidated. This study investigated the effects of NBP on rodents with acute and chronic hypobaric hypoxia.

Methods: Sprague-Dwaley rats and Kunming mice administered with NBP (0, 60, 120, and 240 mg/kg for rats and 0, 90, 180, and 360 mg/kg for mice) were placed in a hypobaric hypoxia chamber at 10,000 m and the survival percentages at 30 min were determined. Then, the time and distance to exhaustion of drug-treated rodents were evaluated during treadmill running and motor-driven wheel-track treadmill experiments, conducted at 5800 m for 3 days or 20 days, to evaluate changes in physical functions. The frequency of active escapes and duration of active escapes were also determined for rats in a shuttle-box experiment, conducted at 5800 m for 6 days or 27 days, to evaluate changes in learning and memory function. ATP levels were measured in the gastrocnemius muscle and malonaldehyde (MDA), superoxide dismutase (SOD), hydrogen peroxide (HO), glutathione peroxidase (GSH-Px), and lactate were detected in sera of rats, and routine blood tests were also performed.

Results: Survival analysis at 10,000 m indicated NBP could improve hypoxia tolerance ability. The time and distance to exhaustion for mice (NBP, 90 mg/kg) and time to exhaustion for rats (NBP, 120 and 240 mg/kg) significantly increased under conditions of acute hypoxia compared with control group. NBP treatment also significantly increased the time to exhaustion for rats when exposed to chronic hypoxia. Moreover, 240 mg/kg NBP significantly increased the frequency of active escapes under conditions of acute hypoxia. Furthermore, the levels of MDA and HO decreased but those of SOD and GSH-Px in the sera of rats increased under conditions of acute and chronic hypoxia. Additionally, ATP levels in the gastrocnemius muscle significantly increased, while lactate levels in sera significantly decreased.

Conclusion: NBP improved physical and learning and memory functions in rodents exposed to acute or chronic hypobaric hypoxia by increasing their anti-oxidative capacity and energy supply.
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http://dx.doi.org/10.1186/s40779-021-00314-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7993509PMC
March 2021

Conservation and trans-regulation of histone modification in the A and B subgenomes of polyploid wheat during domestication and ploidy transition.

BMC Biol 2021 03 9;19(1):42. Epub 2021 Mar 9.

Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.

Background: Polyploidy has played a prominent role in the evolution of plants and many other eukaryotic lineages. However, how polyploid genomes adapt to the abrupt presence of two or more sets of chromosomes via genome regulation remains poorly understood. Here, we analyzed genome-wide histone modification and gene expression profiles in relation to domestication and ploidy transition in the A and B subgenomes of polyploid wheat.

Results: We found that epigenetic modification patterns by two typical euchromatin histone markers, H3K4me3 and H3K27me3, for the great majority of homoeologous triad genes in A and B subgenomes were highly conserved between wild and domesticated tetraploid wheats and remained stable in the process of ploidy transitions from hexaploid to extracted tetraploid and then back to resynthesized hexaploid. However, a subset of genes was differentially modified during tetraploid and hexaploid wheat domestication and in response to ploidy transitions, and these genes were enriched for particular gene ontology (GO) terms. The extracted tetraploid wheat manifested higher overall histone modification levels than its hexaploid donor, and which were reversible and restored to normal levels in the resynthesized hexaploid. Further, while H3K4me3 marks were distally distributed along each chromosome and significantly correlated with subgenome expression as expected, H3K27me3 marks showed only a weak distal bias and did not show a significant correlation with gene expression.

Conclusions: Our results reveal overall high stability of histone modification patterns in the A and B subgenomes of polyploid wheat during domestication and in the process of ploidy transitions. However, modification levels of a subset of functionally relevant genes in the A and B genomes were trans-regulated by the D genome in hexaploid wheat.
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http://dx.doi.org/10.1186/s12915-021-00985-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7944620PMC
March 2021

The potential role of plasma fibroblast growth factor 21 as a diagnostic biomarker for abdominal aortic aneurysm presence and development.

Life Sci 2021 Jun 10;274:119346. Epub 2021 Mar 10.

Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China. Electronic address:

Aims: Fibroblast growth factor 21 (FGF21) has been identified as the master hormonal regulator of energy balance, its elevation is observed in a series of metabolic and cardiovascular diseases. Studies have implicated the role of FGF21 signaling in the pathogenesis of abdominal aortic aneurysm (AAA). We will investigate the association of FGF21 and AAA development.

Materials And Methods: In this study, we assayed plasma levels of FGF21 in 82 patients with AAA and 44 control subjects, then analyzed their relationship with clinical, biochemical and histological phenotypes. The expression of β-klotho, an essential co-receptor of FGF21, was assessed with IHC staining and RT-qPCR. Machine learning models incorporate a combination of FGF21 and clinical data were utilized in the prediction of AAA occurrence.

Key Findings: FGF21 was statistically higher in patients with AAA (781 pg/ml [533, 1213]) than in control subjects (567 pg/ml [324, 939]). After adjustment for age and BMI, we found a positive association of FGF21 levels with AAA diameters, hypertension rate and hsCRP, and a negative correlation between FGF21 levels and HDL-c. Furthermore, the protein levels of β-klotho in abdominal aorta of AAA were found significantly lower than in control group indicating the presence of FGF21 resistance. Combining FGF21 levels with four clinical characteristics significantly improved the stratification of AAA and control groups with an AUC of 0.778.

Significance: Combining detection of plasma FGF21 and clinical characteristics may be reliable for identifying the presence of AAA. The role of FGF21 as a therapeutic target of AAA warrants further investigation.
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http://dx.doi.org/10.1016/j.lfs.2021.119346DOI Listing
June 2021

Evolutionary Contribution of Duplicated Genes to Genome Evolution in the Ginseng Species Complex.

Genome Biol Evol 2021 May;13(5)

Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China.

Genes duplicated by whole genome duplication (WGD) and small-scale duplication (SSD) have played important roles in adaptive evolution of all flowering plants. However, it still remains underinvestigated how the distinct models of duplication events and their contending evolutionary patterns have shaped the genome and epigenomes of extant plant species. In this study, we investigated the contribution of the WGD- and SSD-derived duplicate genes to the genome evolution of one diploid and three closely related allotetraploid Panax species based on genome, methylome, and proteome data sets. Our genome-wide comparative analyses revealed that although the ginseng species complex was recently diverged, they have evolved distinct overall patterns of nucleotide variation, cytosine methylation, and protein-level expression. In particular, genetic and epigenetic asymmetries observed in the recent WGD-derived genes are largely consistent across the ginseng species complex. In addition, our results revealed that gene duplicates generated by ancient WGD and SSD mechanisms exhibited distinct evolutionary patterns. We found the ancient WGD-derived genes (i.e., ancient collinear gene) are genetically more conserved and hypomethylated at the cytosine sites. In contrast, some of the SSD-derived genes (i.e., dispersal duplicated gene) showed hypermethylation and high variance in nucleotide variation pattern. Functional enrichment analyses of the duplicated genes indicated that adaptation-related traits (i.e., photosynthesis) created during the distant ancient WGDs are further strengthened by both the more recent WGD and SSD. Together, our findings suggest that different types of duplicated genes may have played distinct but relaying evolutionary roles in the polyploidization and speciation processes in the ginseng species complex.
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http://dx.doi.org/10.1093/gbe/evab051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8103499PMC
May 2021

[Treatment of Concomitant Intra-abdominal Malignancy and Abdominal Aortic Aneurysm].

Zhongguo Yi Xue Ke Xue Yuan Xue Bao 2021 Feb;43(1):37-41

Department of Vascular Surgery,PUMC Hospital,CAMS and PUMC,Beijing 100730,China.

Objective To explore the outcomes in patients who receive the endovascular abdominal aortic aneurysm repair(EVAR)and have concomitant intra-abdominal malignancy.Methods Between January 2014 and December 2019,all the patients who underwent surgery for malignancy and/or EVAR were retrospectively reviewed.Results Twenty-eight abdominal aortic aneurysm(AAA)patients with concomitant intra-abdominal malignancy were included.The patients were treated by two-stage operation and the priority was given for EVAR in 21 patients.There was no perioperative death or major complications.In the follow-up,one patient developed graft thrombosis and one had type Ⅱ endoleak.There was no AAA-associated death.Conclusions It is preferred that EVAR should come first followed by operation for malignancy.Details of treatment strategy still need further investigation.
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http://dx.doi.org/10.3881/j.issn.1000-503X.12597DOI Listing
February 2021

Association of Epicardial Fat Volume With Increased Risk of Obstructive Coronary Artery Disease in Chinese Patients With Suspected Coronary Artery Disease.

J Am Heart Assoc 2021 Mar 4;10(6):e018080. Epub 2021 Mar 4.

Department of Nuclear Medicine The Third Affiliated Hospital of Soochow University Changzhou Jiangsu Province China.

Background Epicardial adipose tissue may be associated with the pathogenesis of coronary artery disease (CAD), but its effect on obstructive CAD risk is uncertain. Therefore, we aimed to examine the relationship between epicardial adipose tissue and obstructive CAD in Chinese patients with suspected CAD. Methods and Results The present study enrolled 194 consecutive inpatients with suspected CAD who underwent both noncontrast computed tomography and coronary angiography. We measured epicardial fat volume (EFV) and evaluated its association with obstructive CAD, which was defined as coronary stenosis severity ≥70%. Overall, 44.3% patients had obstructive CAD and tend to have higher EFV. Age, body mass index, triglycerides, incidence of hypertension, and hyperlipidemia were higher across tertiles of EFV ( for trend <0.05). In univariate regression analysis, a per-SD increase in EFV was independently associated with obstructive CAD (odds ratio [OR], 2.31; 95% CI, 1.61-3.32; <0.001). Consistent with these findings, EFV was still significantly related to obstructive CAD as continuous variable after adjustment for all traditional risk factors and coronary artery calcium (OR per SD, 2.82; 95% CI, 1.68-4.74; <0.001). Generalized additive model indicated that EFV was linearly associated with risk of obstructive CAD. -value analysis suggested robustness to unmeasured confounding. Conclusions Our results suggested that in Chinese patients with suspected CAD, EFV was significantly and positively associated with the risk of obstructive CAD, independent of traditional risk factors and coronary artery calcium.
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http://dx.doi.org/10.1161/JAHA.120.018080DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8174213PMC
March 2021

Mutation of a major CG methylase alters genome-wide lncRNA expression in rice.

G3 (Bethesda) 2021 Apr;11(4)

Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China.

Plant long non-coding RNAs (lncRNAs) function in diverse biological processes, and lncRNA expression is under epigenetic regulation, including by cytosine DNA methylation. However, it remains unclear whether 5-methylcytosine (5mC) plays a similar role in different sequence contexts (CG, CHG, and CHH). In this study, we characterized and compared the profiles of genome-wide lncRNA profiles (including long intergenic non-coding RNAs [lincRNAs] and long noncoding natural antisense transcripts [lncNATs]) of a null mutant of the rice DNA methyltransferase 1, OsMET1-2 (designated OsMET1-2-/-) and its isogenic wild type (OsMET1-2+/+). The En/Spm transposable element (TE) family, which was heavily methylated in OsMET1-2+/+, was transcriptionally de-repressed in OsMET1-2-/- due to genome-wide erasure of CG methylation, and this led to abundant production of specific lncRNAs. In addition, RdDM-mediated CHH hypermethylation was increased in the 5'-upstream genomic regions of lncRNAs in OsMET1-2-/-. The positive correlation between the expression of lincRNAs and that of their proximal protein-coding genes was also analyzed. Our study shows that CG methylation negatively regulates the TE-related expression of lncRNA and demonstrates that CHH methylation is also involved in the regulation of lncRNA expression.
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http://dx.doi.org/10.1093/g3journal/jkab049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8049413PMC
April 2021

The Ubiquitin E3 Ligase SR1 Modulates the Submergence Response by Degrading Phosphorylated WRKY33 in Arabidopsis.

Plant Cell 2021 Feb 22. Epub 2021 Feb 22.

Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu 610065, China.

Oxygen deprivation caused by flooding activates acclimation responses to stress and restricts plant growth. After experiencing flooding stress, plants must restore normal growth; however, which genes are dynamically and precisely controlled by flooding stress remains largely unknown. Here, we show that the Arabidopsis thaliana ubiquitin E3 ligase SUBMERGENCE RESISTANT1 (SR1) regulates the stability of the transcription factor WRKY33 to modulate the submergence response. SR1 physically interacts with WRKY33 in vivo and in vitro and controls its ubiquitination and proteasomal degradation. Both the sr1 mutant and WRKY33 overexpressors exhibited enhanced submergence tolerance and enhanced expression of hypoxia-responsive genes. Genetic experiments showed that WRKY33 functions downstream of SR1 during the submergence response. Submergence induced the phosphorylation of WRKY33, which enhanced the activation of RAP2.2, a positive regulator of hypoxia-response genes. Phosphorylated WRKY33 and RAP2.2 were degraded by SR1 and the N-degron pathway during reoxygenation, respectively. Taken together, our findings reveal that the on-and-off module SR1-WRKY33-RAP2.2 is connected to the well-known N-degron pathway to regulate acclimation to submergence in Arabidopsis. These two different but related modulation cascades precisely balance submergence acclimation with normal plant growth.
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http://dx.doi.org/10.1093/plcell/koab062DOI Listing
February 2021

Weighted Gene Co-expression Network Analysis Identifies Crucial Genes Mediating Progression of Carotid Plaque.

Front Physiol 2021 5;12:601952. Epub 2021 Feb 5.

Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.

Background: Surface rupture of carotid plaque can cause severe cerebrovascular disease, including transient ischemic attack and stroke. The aim of this study was to elucidate the molecular mechanism governing carotid plaque progression and to provide candidate treatment targets for carotid atherosclerosis.

Methods: The microarray dataset GSE28829 and the RNA-seq dataset GSE104140, which contain advanced plaque and early plaque samples, were utilized in our analysis. Differentially expressed genes (DEGs) were screened using the "limma" R package. Gene modules for both early and advanced plaques were identified based on co-expression networks constructed by weighted gene co-expression network analysis (WGCNA). Gene Ontology (GO) and Kyoto Encyclopedia of Genes Genomes (KEGG) analyses were employed in each module. In addition, hub genes for each module were identified. Crucial genes were identified by molecular complex detection (MCODE) based on the DEG co-expression network and were validated by the GSE43292 dataset. Gene set enrichment analysis (GSEA) for crucial genes was performed. Sensitivity analysis was performed to evaluate the robustness of the networks that we constructed.

Results: A total of 436 DEGs were screened, of which 335 were up-regulated and 81 were down-regulated. The pathways related to inflammation and immune response were determined to be concentrated in the black module of the advanced plaques. The hub gene of the black module was (Rho GTPase activating protein 18). (neutrophil cytosolic factor 2), (IQ motif containing GTPase activating protein 2) and (CD86 molecule) had the highest connectivity among the crucial genes. All crucial genes were validated successfully, and sensitivity analysis demonstrated that our results were reliable.

Conclusion: To the best of our knowledge, this study is the first to combine DEGs and WGCNA to establish a DEG co-expression network in carotid plaques, and it proposes potential therapeutic targets for carotid atherosclerosis.
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http://dx.doi.org/10.3389/fphys.2021.601952DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7894049PMC
February 2021

Incremental value of epicardial fat volume to coronary artery calcium score and traditional risk factors for predicting myocardial ischemia in patients with suspected coronary artery disease.

J Nucl Cardiol 2021 Feb 19. Epub 2021 Feb 19.

Department of Nuclear Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu Province, China.

Background: Epicardial fat volume (EFV) has been reported to be associated with coronary artery disease (CAD). CAD is the leading cause of myocardial ischemia and myocardial ischemia is closely related to major adverse cardiovascular events. We hypothesized that EFV could provide incremental value to traditional risk factors and coronary artery calcium score (CACS) in predicting myocardial ischemia in Chinese patients with suspected CAD.

Methods: We retrospectively studied 204 Chinese patients with suspected CAD who underwent single-photon emission computerized tomography-myocardial perfusion imaging (SPECT-MPI) combined with computed tomography (CT). Pericardial contours were manually defined, and EFV was automatically calculated. A reversible perfusion defect with summed difference score (SDS) ≥ 2 was defined as myocardial ischemia.

Results: The myocardial ischemia group had higher EFV than normal MPI group (137.80 ± 34.95cm vs. 106.63 ± 29.10 cm, P < .001). In multivariable logistic regression analysis, high EFV was significantly associated with myocardial ischemia [odds ratio (OR): 8.30, 95% CI: 3.72-18.49, P < .001]. Addition of EFV to CACS and traditional risk factors could predict myocardial ischemia more effectively, with larger AUC .82 (P < .001), positive net reclassification index .14 (P = .04) and integrated discrimination improvement .14 (P < .001). The bootstrap resampling method (times = 500) was used to internally validation and calculate the 95% confidence interval (CI) of the AUC (95% CI .75-.87). The calibration curve for the probability of myocardial ischemia demonstrated good agreement between prediction and observation.

Conclusions: In Chinese patients with suspected CAD, EFV was significantly associated with myocardial ischemia, and improved prediction of myocardial ischemia above traditional risk factors and CACS.
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http://dx.doi.org/10.1007/s12350-021-02538-5DOI Listing
February 2021

Inhibition of CXCR2 alleviates the development of abdominal aortic aneurysm in Apo E-/- mice.

Acta Cir Bras 2021 15;36(1):e360105. Epub 2021 Feb 15.

PhD. Weifang People's Hospital - Department of Vascular Surgery - Weifang, Shandong, China.

Purpose: To investigate the relationship between atherosclerotic abdominal aortic aneurysm (AAA) and CXC chemokine receptor type 2 (CXCR2).

Methods: Mouse AAA model was established by embedding angiotensin-II pump (1000 ng/kg/min) in ApoE-/- mice. Mice were received SB225002, a selective CXCR2 antagonist, for treatment. Blood pressure was recorded, and CXCR2+ macrophages were examined by flow cytometry analysis. Terminal-deoxynucleotidyl transferase mediated nick end labeling (TUNEL) staining was performed to detect cell apoptosis of abdominal aortic aneurysms. Macrophages were isolated from ApoE-/- mice and treated with Ang II and/or SB225002. Dihydroethidium staining was carried out to determine reactive oxygen species (ROS) activity. Enzyme-linked immunosorbent assay (ELISA) was performed to determine the production of IL-1β and TNF-α. The corresponding gene expressions were measured using real-time polymerase chain reaction (PCR), western blot, and immunohistochemistry staining.

Results: We found that Ang II activated the expression of CXCR2 in monocytes during the formation of AAA. Inhibition of CXCR2 significantly reduced the size of AAA, attenuated inflammation and phenotypic changes in blood vessels. Ang II-induced macrophages exhibited elevated ROS activity, and elevated levels of 1β and TNF-α, which were then partly abolished by SB225002.

Conclusions: CXCR2 plays an important role in AAA, suggesting that inhibiting CXCR2 may be a new treatment for AAA.
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http://dx.doi.org/10.1590/ACB360105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7892195PMC
February 2021

Enhanced removal of As(III) and As(V) from water by a novel zirconium-chitosan modified spherical sodium alginate composite.

Int J Biol Macromol 2021 Apr 12;176:304-314. Epub 2021 Feb 12.

School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, PR China; Research Center of Analysis and Test, East China University of Science and Technology, Shanghai 200237, PR China. Electronic address:

Most nano-scaled adsorbents have trouble in separating from aqueous solution, thus, a need for new materials of facile separation and predominant adsorption performance has arisen. This present study focused on a novel segregative zirconium-chitosan modified sodium alginate (Zr-CTS/SA) composite preparation and its performance for As(III/V) removal from aqueous solution. The obtained composite presented a spherical structure with a diameter of 2.0-3.0 mm and favorable thermal stability. Experimental data showed that Zr-CTS/SA had considerable adsorbability for As(III) and As(V), the adsorption capacities were enhanced about at least 20 and 6 times separately compared with pristine SA beads. The adsorption processes of As(III) and As(V) could both be described with Langmuir isotherm model and the maximum adsorption capacities reached 43.19 and 76.78 mg g, respectively. The kinetic data of As(III) followed the intra-particle diffusion model while As(V) fitted the pseudo-first-order model. Moreover, the adsorption mechanisms of As(III/V) involved ligand exchange with Cl on the surface of Zr-CTS/SA, another reaction pathway for As(V) was the electrostatic attraction with protonated -OH and -NH groups. Note that the employment of Zr-CTS/SA in low-concentration arsenic solution exhibited a residue concentration as low as the 10 μg L WHO guideline for drinking water.
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http://dx.doi.org/10.1016/j.ijbiomac.2021.02.077DOI Listing
April 2021

Treatment of venous thromboembolism in cancer patients: a systematic review and meta-analysis on the efficacy and safety of different direct oral anticoagulants (DOACs).

Ann Transl Med 2021 Jan;9(2):162

Department of Vascular Surgery, Peking Union Medical College Hospital, Beijing, China.

Background: To evaluate the efficacy and safety of different direct oral anticoagulants (DOACs) compared with low molecular weight heparins (LMWHs) in the treatment of venous thromboembolism (VTE) in cancer patients.

Methods: Literature was searched in databases including Cochrane Library, EMBASE (Ovid), and MEDLINE (PubMed). Eligible studies were included, and data were collected independently by 2 reviewers. We conducted a systematic review of the efficacy and safety of DOACs in the treatment of VTE in cancer patients. The odds ratios (ORs) of different DOACs compared with LMWHs for VTE, deep vein thrombosis (DVT), pulmonary embolism (PE) recurrence, major bleeding, and clinically relevant non-major bleeding (CRNMB), were calculated in meta-analyses and subgroup analyses.

Results: A total of 18 articles were eligible for analyses, including 4 randomized controlled trials (RCTs) and 14 retrospective studies. Both RCTs and retrospective studies confirmed that DOACs decreased the risk of VTE recurrence [RCTs: OR, 0.60; 95% confidence interval (CI), 0.45-0.80; retrospective studies: OR, 0.73; 95% CI, 0.59-0.90] and DVT recurrence (RCTs: OR, 0.54; 95% CI, 0.36-0.80; retrospective studies: OR, 0.20; 95% CI, 0.06-0.63), but not PE recurrence or fatal PE in cancer patients. Subgroup analyses revealed an important role of rivaroxaban in decreasing recurrent VTE. Meanwhile, major bleeding events were not increased in the DOAC group, but the risks of CRNMBs were significantly elevated. Subgroup analyses confirmed the role of rivaroxaban in increasing the risk of major bleeding events and CRNMBs.

Conclusions: Compared with LMWHs, DOACs (especially rivaroxaban) significantly reduce the risk of VTE and DVT, but not PE recurrence, in patients with cancer. Although DOACs did not increase the major bleeding events in pooled analysis, rivaroxaban showed an elevated risk of this adverse effect in subgroup analysis. In addition, the risk of CRNMB events was increased after the application of DOACs including rivaroxaban.
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http://dx.doi.org/10.21037/atm-20-8156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7867886PMC
January 2021

Identification of crucial genes mediating abdominal aortic aneurysm pathogenesis based on gene expression profiling of perivascular adipose tissue by WGCNA.

Ann Transl Med 2021 Jan;9(1):52

Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.

Background: With a mortality rate of 65-85%, a ruptured abdominal aortic aneurysm (AAA) can have catastrophic consequences for patients. However, few effective pharmaceutical treatments are available to treat this condition. Therefore, elucidating the pathogenesis of AAA and finding the potential molecular targets for medical therapies are vital lines of research.

Methods: An mRNA microarray dataset of perivascular adipose tissue (PVAT) in AAA patients was downloaded and differentially expressed gene (DEG) screening was performed. Weighted gene co-expression networks for dilated and non-dilated PVAT samples were constructed via weighted correlation network analysis (WGCNA) and used to detect gene modules. Functional annotation analysis was performed for the DEGs and gene modules. We identified the hub genes of the modules and created a DEG co-expression network. We then mined crucial genes based on this network using Molecular Complex Detection (MCODE) in Cytoscape. Crucial genes with top-6 degree in the crucial gene cluster were visualized, and their potential clinical significance was determined.

Results: Of the 173 DEGs screened, 99 were upregulated and 74 were downregulated. Co-expression networks were built and we detected 6 and 5 modules for dilated and non-dilated PVAT samples, respectively. The turquoise and black modules for dilated PVAT samples were related to inflammation and immune response. and were the hub genes of these 2 modules, respectively. Then a DEG co-expression network with 112 nodes and 953 edges was created. was the crucial gene with the highest connectivity and showed potential clinical significance.

Conclusions: Using WGCNA, gene modules were detected and hub genes and crucial genes were identified. These crucial genes might be potential targets for pharmaceutic therapies and have potential clinical significance. Future and experiments are required to more comprehensively explore the biological mechanisms by which these genes affect AAA pathogenesis.
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http://dx.doi.org/10.21037/atm-20-3758DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7859787PMC
January 2021

Longitudinal evaluation of diastolic dyssynchrony by SPECT gated myocardial perfusion imaging early after acute myocardial infarction and the relationship with left ventricular remodeling progression in a swine model.

J Nucl Cardiol 2021 Jan 27. Epub 2021 Jan 27.

Department of Nuclear Medicine, The Third Affiliated Hospital of Soochow University, No. 185, Juqian Street, Changzhou, 213003, Jiangsu Province, China.

Background: Left ventricular diastolic dyssynchrony (LVDD), a dyssynchronous relaxation pattern, has been known to develop after myocardial damage. We aimed to evaluate the dynamic changes in LVDD in the early stage of acute myocardial infarction (AMI) by phase analysis of technetium methoxyisobutylisonitrile (Tc-MIBI) single-photon emission computed tomography (SPECT) gated myocardial perfusion imaging (GMPI) and explore its relationship with the progression of left ventricular remodeling (LVR).

Methods: The left anterior descending coronary arteries of 16 Bama miniature swine were occluded with a balloon to build AMI models. Animals were imaged by SPECT GMPI before AMI and at 1 day, 1 week and 4 weeks after AMI, and quantitative analysis was performed to determine the extent of left ventricle (LV) perfusion defects, left ventricular systolic dyssynchrony (LVSD) and the LVDD parameters: phase histogram bandwidth (PBW) and phase standard deviation (PSD). Echocardiography was simultaneously applied to evaluate left ventricular end-diastolic volume (LVEDV), left ventricular end-systolic volume (LVESV), left ventricular ejection fraction (LVEF), and the LVDD parameters: Te-12-diff and Te-12-SD. Myocardial injury markers were measured, and 12-lead ECGs were performed. The degree of LVR progression was defined as ΔLVESV (%) = (LVESV - LVESV)/LVESV.

Results: Thirteen swine completed the study. LVDD parameters changed dynamically at different time points after AMI. LVDD occurred as early as 1 day after AMI, peaked at 1 week, and trended toward a partial recovery at 4 weeks. Phase analysis on SPECT GMPI showed a significant correlation with tissue Doppler imaging for the assessment of LVDD during the longitudinal evaluation (r = 0.569 to 0.787, both P <0.05). During the univariate and multivariate regression analyses, the LVDD parameters PBW and PSD as of 1 day after AMI were significantly associated with the progression of LVR, respectively (PBW, β = 0.004, 95% CI 0.001 to 0.007, P = 0.024; PSD, β = 0.008, 95% CI 0.000 to 0.017, P = 0.049). Adjusted smooth curve fitting and threshold effect analysis indicated PBW and PSD break-point values of 142° and 60.4°, respectively, to predict the progression of LVR after AMI.

Conclusions: Phase analysis of SPECT GMPI can accurately and reliably characterize LVDD. LVDD occurred on the first day after AMI, reached its peak at 1 week, and partially recovered at 4 weeks after AMI. LVDD as evaluated by phase analysis of SPECT GMPI early after AMI was significantly associated with the progression of LVR. The early assessment of LVDD after AMI may provide helpful information for predicting the progression of LVR in the future.
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http://dx.doi.org/10.1007/s12350-020-02483-9DOI Listing
January 2021

CHYR1 ubiquitinates the phosphorylated WRKY70 for degradation to balance immunity in Arabidopsis thaliana.

New Phytol 2021 05 16;230(3):1095-1109. Epub 2021 Feb 16.

Key Laboratory for Bio-resources and Eco-environment, College of Life Science & State Key, Laboratory of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu, 610065, China.

It is critically important for plants to control the trade-off between normal growth and pathogen immunity. However, the underlying molecular mechanism remains largely unknown. Here we report such a mechanism controlled by WRKY70 and its partner CHYR1 in Arabidopsis. We found that both levels of the WRKY70 target gene SARD1 and the phosphorylated forms of WRKY70 were increased in WRKY70OE plants upon Pst DC3000 infection. Mechanistically, phosphorylation of WRKY70 at Thr22 and Ser34 occurs, which then activates SARD1 expression through binding to a WT box. Phosphorylated WRKY70 is degraded by 26S proteasome via CHYR1 when resuming normal growth after infection. In addition, nonphosphorylated WRKY70 represses SARD1 expression by binding to both W (inhibitory activity site) and WT (active activity site) boxes. The binding of WRKY70 to alternative cis-elements of SARD1 through a phosphorylation-mediated switch controlled by CHYR1 contributes to modulating the balance between immunity and growth.
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http://dx.doi.org/10.1111/nph.17231DOI Listing
May 2021

JMJ17-WRKY40 and HY5-ABI5 modules regulate the expression of ABA-responsive genes in Arabidopsis.

New Phytol 2021 04 12;230(2):567-584. Epub 2021 Feb 12.

Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.

Abscisic acid (ABA) plays a crucial role in the adaptation of young seedlings to environmental stresses. However, the role of epigenetic components and core transcriptional machineries in the effect of ABA on seed germination and seedling growth remain unclear. Here, we show that a histone 3 lysine 4 (H3K4) demethylase, JMJ17, regulates the expression of ABA-responsive genes during seed germination and seedling growth. Using comparative interactomics, WRKY40, a central transcriptional repressor in ABA signaling, was shown to interact with JMJ17. WRKY40 facilitates the recruitment of JMJ17 to the ABI5 chromatin, which removes gene activation marks (H3K4me3) from the ABI5 chromatin, thereby repressing its expression. Additionally, WRKY40 represses the transcriptional activation activity of HY5, which can activate ABI5 expression by directly binding to its promoter. An increase in ABA concentrations decreases the affinity of WRKY40 for the ABI5 promoter. Thus, WRKY40 and JMJ17 are released from the ABI5 chromatin, activating HY5. The accumulated ABI5 protein further shows heteromeric interaction with HY5, and thus synergistically activates its own expression. Our findings reveal a novel transcriptional switch, composed of JMJ17-WRKY40 and HY5-ABI5 modules, which regulates the ABA response during seed germination and seedling development in Arabidopsis.
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http://dx.doi.org/10.1111/nph.17177DOI Listing
April 2021

Six Immune Associated Genes Construct Prognostic Model Evaluate Low-Grade Glioma.

Front Immunol 2020 21;11:606164. Epub 2020 Dec 21.

Department of Neurosurgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China.

Background: The immunotherapy of Glioma has always been a research hotspot. Although tumor associated microglia/macrophages (TAMs) proves to be important in glioma progression and drug resistance, our knowledge about how TAMs influence glioma remains unclear. The relationship between glioma and TAMs still needs further study.

Methods: We collected the data of TAMs in glioma from NCBI Gene Expression Omnibus (GEO) that included 20 glioma samples and 15 control samples from four datasets. Six genes were screened from the Differential Expression Gene through Gene ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, protein-protein interaction (PPI) network and single-cell sequencing analysis. A risk score was then constructed based on the six genes and patients' overall survival rates of 669 patients from The Cancer Genome Atlas (TCGA). The efficacy of the risk score in prognosis and prediction was verified in Chinese Glioma Genome Atlas (CGGA).

Results: Six genes, including CD163, FPR3, LPAR5, P2ry12, PLAUR, SIGLEC1, that participate in signal transduction and plasma membrane were selected. Half of them, like CD163, FPR3, SIGLEC1, were mainly expression in M2 macrophages. FPR3 and SIGLEC1 were high expression genes in glioma associated with grades and IDH status. The overall survival rates of the high risk score group was significantly lower than that of the low risk score group, especially in LGG.

Conclusion: Joint usage of the 6 candidate genes may be an effective method to diagnose and evaluate the prognosis of glioma, especially in Low-grade glioma (LGG).
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http://dx.doi.org/10.3389/fimmu.2020.606164DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7779629PMC
June 2021

The complete chloroplast genome of (Hamamelidaceae).

Mitochondrial DNA B Resour 2020 Jan 16;5(1):695-696. Epub 2020 Jan 16.

College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.

is a semi-evergreen broad-leaved tree species distributed in southern China. In 1999, it was approved and published as a national secondary protected plant. We obtained the complete chloroplast genome sequence of by Illumina sequencing data. The complete chloroplast sequence is 160,430 bp, include large single-copy (LSC) region of 88,991 bp, small single-copy (SSC) region of 18,917 bp, and a pair of invert repeats (IR) regions of 26,261 bp. Plastid genome contain 133 genes, 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis showed that is closely related to
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http://dx.doi.org/10.1080/23802359.2020.1714502DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7748583PMC
January 2020