Publications by authors named "Xiaowu Wang"

149 Publications

Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids.

Plant Biotechnol J 2021 Jul 26. Epub 2021 Jul 26.

School of Biological Sciences and the Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, WA, Australia.

Plant genomes demonstrate significant presence/absence variation (PAV) within a species; however, the factors that lead to this variation have not been studied systematically in Brassica across diploids and polyploids. Here, we developed pangenomes of polyploid Brassica napus and its two diploid progenitor genomes B. rapa and B. oleracea to infer how PAV may differ between diploids and polyploids. Modelling of gene loss suggests that loss propensity is primarily associated with transposable elements in the diploids while in B. napus, gene loss propensity is associated with homoeologous recombination. We use these results to gain insights into the different causes of gene loss, both in diploids and following polyploidization, and pave the way for the application of machine learning methods to understanding the underlying biological and physical causes of gene presence/absence.
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http://dx.doi.org/10.1111/pbi.13674DOI Listing
July 2021

Impacts of allopolyploidization and structural variation on intraspecific diversification in Brassica rapa.

Genome Biol 2021 05 31;22(1):166. Epub 2021 May 31.

Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing, 100081, China.

Background: Despite the prevalence and recurrence of polyploidization in the speciation of flowering plants, its impacts on crop intraspecific genome diversification are largely unknown. Brassica rapa is a mesopolyploid species that is domesticated into many subspecies with distinctive morphotypes.

Results: Herein, we report the consequences of the whole-genome triplication (WGT) on intraspecific diversification using a pan-genome analysis of 16 de novo assembled and two reported genomes. Among the genes that derive from WGT, 13.42% of polyploidy-derived genes accumulate more transposable elements and non-synonymous mutations than other genes during individual genome evolution. We denote such genes as being "flexible." We construct the Brassica rapa ancestral genome and observe the continuing influence of the dominant subgenome on intraspecific diversification in B. rapa. The gene flexibility is biased to the more fractionated subgenomes (MFs), in contrast to the more intact gene content of the dominant LF (least fractionated) subgenome. Furthermore, polyploidy-derived flexible syntenic genes are implicated in the response to stimulus and the phytohormone auxin; this may reflect adaptation to the environment. Using an integrated graph-based genome, we investigate the structural variation (SV) landscapes in 524 B. rapa genomes. We observe that SVs track morphotype domestication. Four out of 266 candidate genes for Chinese cabbage domestication are speculated to be involved in the leafy head formation.

Conclusions: This pan-genome uncovers the possible contributions of allopolyploidization on intraspecific diversification and the possible and underexplored role of SVs in favorable trait domestication. Collectively, our work serves as a rich resource for genome-based B. rapa improvement.
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http://dx.doi.org/10.1186/s13059-021-02383-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8166115PMC
May 2021

Genome structural evolution in Brassica crops.

Nat Plants 2021 06 27;7(6):757-765. Epub 2021 May 27.

Department of Biology, University of York, York, UK.

The cultivated Brassica species include numerous vegetable and oil crops of global importance. Three genomes (designated A, B and C) share mesohexapolyploid ancestry and occur both singly and in each pairwise combination to define the Brassica species. With organizational errors (such as misplaced genome segments) corrected, we showed that the fundamental structure of each of the genomes is the same, irrespective of the species in which it occurs. This enabled us to clarify genome evolutionary pathways, including updating the Ancestral Crucifer Karyotype (ACK) block organization and providing support for the Brassica mesohexaploidy having occurred via a two-step process. We then constructed genus-wide pan-genomes, drawing from genes present in any species in which the respective genome occurs, which enabled us to provide a global gene nomenclature system for the cultivated Brassica species and develop a methodology to cost-effectively elucidate the genomic impacts of alien introgressions. Our advances not only underpin knowledge-based approaches to the more efficient breeding of Brassica crops but also provide an exemplar for the study of other polyploids.
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http://dx.doi.org/10.1038/s41477-021-00928-8DOI Listing
June 2021

CAP Analysis of the Distribution of the Introduced Bemisia tabaci (Hemiptera: Aleyrodidae) Species Complex in Xinjiang, China and the Southerly Expansion of the Mediterranean Species.

J Insect Sci 2021 Mar;21(2)

Institute of Microbial Application, Xinjiang Academy of Agricultural Sciences, Xinjiang, China.

Bemisia tabaci (Gennadius) cryptic complex has invaded Xinjiang, China, since 1998. The distribution of Mediterranean (MED) and Middle East-Asia Minor 1 (MEAM1) B. tabaci substrains has been gradually identified due to the development of molecular technology. In this study, the distribution of MED and MEAM1 in Xinjiang was determined by cleaved amplified polymorphic sequence (CAPs). Results showed that MED dominated in northern Xinjiang (84%), whereas MEAM1 was dominant in southern Xinjiang (72%). Five pairs of simple sequence repeat (SSR) primers were used to analyze the genetic diversity of B. tabaci among 36 geographic populations. The genetic diversity of MED and MEAM1was low and varied little among populations in Xinjiang (0.09 ± 0.14 and 0.09 ± 0.13, respectively). Based on ∆K statistic, 13 populations of MEAM1 could be classified into two subgroups at K = 2, whereas the 23 populations of MED could be classified into four subgroups at K = 4. However, Mantel t-test demonstrated no correlation between geographical and genetic distances among B. tabaci complex (R = 0.42, P = 1.00). Neighbor-joining and principal coordinate analysis showed that geographical isolation and interspecific differences were the main causes of the genetic variation. Gene flow predicted that MEAM1 was most likely introduced from Urumqi to the southern Xinjiang. Meanwhile, a large proportion of MED in Kashi region came from Changji and Yining. To block ongoing dispersal, strict detection and flower quarantine regulations need to be enforced.
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http://dx.doi.org/10.1093/jisesa/ieaa151DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8040787PMC
March 2021

Divergence of three BRX homoeologs in Brassica rapa and its effect on leaf morphology.

Hortic Res 2021 Apr 1;8(1):68. Epub 2021 Apr 1.

Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China.

The leafy head characteristic is a special phenotype of Chinese cabbage resulting from artificial selection during domestication and breeding. BREVIS RADIX (BRX) has been suggested to control root elongation, shoot growth, and tiller angle in Arabidopsis and rice. In Brassica rapa, three BrBRX homoeologs have been identified, but only BrBRX.1 and BrBRX.2 were found to be under selection in leaf-heading accessions, indicating their functional diversification in leafy head formation. Here, we show that these three BrBRX genes belong to a plant-specific BRX gene family but that they have significantly diverged from other BRX-like members on the basis of different phylogenetic classifications, motif compositions and expression patterns. Moreover, although the expression of these three BrBRX genes differed, compared with BrBRX.3, BrBRX.1, and BrBRX.2 displayed similar expression patterns. Arabidopsis mutant complementation studies showed that only BrBRX.1 could rescue the brx root phenotype, whereas BrBRX.2 and BrBRX.3 could not. However, overexpression of each of the three BrBRX genes in Arabidopsis resulted in similar pleiotropic leaf phenotypes, including epinastic leaf morphology, with an increase in leaf number and leaf petiole length and a reduction in leaf angle. These leaf traits are associated with leafy head formation. Further testing of a SNP (T/C) in BrBRX.2 confirmed that this allele in the heading accessions was strongly associated with the leaf-heading trait of B. rapa. Our results revealed that all three BrBRX genes may be involved in the leaf-heading trait, but they may have functionally diverged on the basis of their differential expression.
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http://dx.doi.org/10.1038/s41438-021-00504-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8012600PMC
April 2021

Transcriptome profiling of differentially expressed genes of male and female inflorescences in spinach ( L.).

Genome 2021 Aug 4;64(8):777-788. Epub 2021 Feb 4.

Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing 100081, People's Republic of China.

Spinach ( L.) is commonly considered a dioecious plant with heterogametic (XY) and homogametic (XX) sex chromosomes. The characteristic is also utilized for the production of spinach hybrid seeds. However, the molecular mechanisms of sex determination in spinach are still unclear because of a lack of genomic and transcriptomic information. In this study, RNA sequencing (RNA-seq) was performed in male and female inflorescences to provide insight into the molecular basis of sex determination in spinach. Comparative transcriptome analyses showed that 2278 differentially expressed genes (DEGs) were identified between male and female inflorescences. A high correlation between the RNA-Seq and qRT-PCR validation for DEGs was observed. Among these, 182 DEGs were annotated to transcription factors including the MYB family protein, bHLH family, and MADS family, suggesting these factors might play a vital role in sex determination. Moreover, 26 DEGs related to flower development, including nine ABCE class genes, were detected. Expression analyses of hormone pathways showed that brassinosteroids may be key hormones related to sex determination in spinach. Overall, this study provides a large amount of DEGs related to sexual expression and lays a foundation for unraveling the regulatory mechanism of sex determination in spinach.
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http://dx.doi.org/10.1139/gen-2020-0122DOI Listing
August 2021

Novel PGC-1/ATF5 Axis Partly Activates UPR and Mediates Cardioprotective Role of Tetrahydrocurcumin in Pathological Cardiac Hypertrophy.

Oxid Med Cell Longev 2020 26;2020:9187065. Epub 2020 Dec 26.

Department of Cardiovascular Surgery, Xijing Hospital, The Fourth Military Medical University, 127 Changle West Road, Xi'an, 710032, China.

Mitochondrial unfolding protein response (UPR) effectively resists the pathological cardiac hypertrophy and improves the mitochondrial function. However, the specific activation mechanism and drugs that can effectively activate UPR in the cardiac muscle are yet to be elucidated. The aim of this study was to determine the regulation role of UPR on preventing pathological cardiac hypertrophy by tetrahydrocurcumin (THC) and explore its underlying molecular mechanism. Male C57BL/6J wild-type (WT) mice were divided into a control group and subjected to sham treatment for 4 weeks, and a test group which was subjected to transverse aortic constriction (TAC) surgery. Animals in the control and test group were orally administered THC (50 mg/kg) for 4 weeks after TAC procedure; an equivalent amount of saline was orally administered in the control sham-treated group and the TAC group. Subsequently, oxidative stress and UPR markers were assessed in these mice, and cardiac hypertrophy, fibrosis, and cardiac function were tested. Small interfering RNA (siRNA) targeting proliferator-activated receptor-gamma coactivator (PGC)-1 and activating transcription factor 5 (ATF5) were used to determine the UPR activation mechanism. THC supplement partly upregulated UPR effectors and inhibited TAC-induced oxidative stress compared with TAC-operated WT mice, thereby substantially attenuating contractile dysfunction, cardiac hypertrophy, and fibrosis. Furthermore, PGC-1 knockdown blunted the UPR activation and the cardioprotective role of THC. The interaction between PGC-1 and ATF5 was tested in neonatal rat cardiac myocytes under normal conditions. The results showed that PGC-1 was an upstream effector of ATF5 and partly activated UPR. In vitro, phenylephrine- (PE-) induced cardiomyocyte hypertrophy caused ATF5 upregulating rather than downregulating corresponding to the downregulation of PGC-1. The PGC-1/ATF5 axis mediated the UPR activation and stress-resistance role of THC in vitro. Collectively, the present study provides the first evidence that PGC-1 and ATF5 can form a signaling axis to partly activate UPR that mediates the cardioprotective role of THC in pathological cardiac hypertrophy.
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http://dx.doi.org/10.1155/2020/9187065DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7781724PMC
September 2021

Comparison of parameter agreement for characterization of corneal subbasal nerve plexus in the whorl-like region and central cornea using in vivo confocal microscopy.

Int Ophthalmol 2021 Feb 9;41(2):559-565. Epub 2020 Nov 9.

Shanxi Eye Hospital, Taiyuan, China.

Purpose: To compare the reliability of the whorl-like region with that of the central cornea for accurate assessment of corneal subbasal nerve plexus (SNP) by analyzing the parameter variability of these two anatomical regions in repeated measurements.

Methods: Participants were scanned in the central cornea and whorl-like region with in vivo confocal microscopy on three occasions by two examiners within a time span of one week. Coefficients of repeatability (CoR), intra-class correlation coefficient (ICC), and Bland-Altman scatter plots with 95% limits of agreement (LOA) in the central cornea and whorl-like region were calculated, respectively, based on the nerve fiber length, then the inter-observer and intra-observer agreement were compared between these two anatomical regions.

Results: The inter-observer ICC was 0.945, the inter-observer CoR was 0.052, the intra-observer ICC was 0.936, and the inter-observer CoR was 0.046, with narrow 95% LOA within 1 standard deviation in the whorl-like region, whereas the inter-observer ICC was 0.600, the inter-observer CoR was 0.207, the intra-observer ICC was 0.206, and the intra-observer CoR was 0.253, with 95% LOA nearly threefold wider than the standard deviation in the central cornea.

Conclusions: Nerve parameter in the whorl-like region showed higher inter-observer and intra-observer agreement than that of the central cornea. The whorl-like region is a more reliable site for accurate assessment of SNP.
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http://dx.doi.org/10.1007/s10792-020-01607-xDOI Listing
February 2021

Improved Brassica oleracea JZS assembly reveals significant changing of LTR-RT dynamics in different morphotypes.

Theor Appl Genet 2020 Nov 9;133(11):3187-3199. Epub 2020 Aug 9.

Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Haidian District, No.12. Zhongguancun South St, Beijing, 100081, China.

Brassica oleracea is an important vegetable crop that has provided ancestor genomes of the two most important Brassica oil crops, Brassica napus and Brassica carinata. The current B. oleracea reference genome (JZS, also named 02-12) displays problems of large mis-assemblies, low sequence continuity, and low assembly integrity, thus limiting genomic analysis. We reported an updated assembly of the B. oleracea reference genome (JZS v2) obtained through single-molecule sequencing and chromosome conformation capture technologies. We assembled an additional 83.16 Mb of genomic sequences, and the updated genome features a contig N50 size of 2.37 Mb, representing an ~ 88-fold improvement. We detected a new round of long terminal repeat retrotransposon (LTR-RT) burst in the new assembly. Comparative analysis with the reported genome sequences of two other genomes of B. oleracea (TO1000 and HDEM) identified extensive gene order and gene structural variation. In addition, we found that the genome-specific amplification of Gypsy-like LTR-RTs occurred around 0-1 million years ago (MYA). In particular, the athila, tat, and Del families were extensively amplified in JZS around 0-1 MYA. Moreover, we identified that the syntenic genes were modified due to the insertion of genome-specific LTR-RTs. These results indicated that the genome-specific LTR-RT dynamics were associated with genome diversification in B. oleracea.
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http://dx.doi.org/10.1007/s00122-020-03664-3DOI Listing
November 2020

An unsymmetrical binuclear iminopyridine-iron complex and its catalytic isoprene polymerization.

Chem Commun (Camb) 2020 Aug;56(62):8846-8849

Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.

A series of chloride-bridged unsymmetrical mixed Fe(ii)-HS/Fe(ii)-LS binuclear structures has been prepared and characterized. Upon activation with MAO, highly efficient catalytic polymerization of isoprene was achieved, delivering an ultra-high molecular weight (catalyst loading = 2.5 ppm, Mn = 1.8 × 106 g mol-1, Mw/Mn = 1.4).
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http://dx.doi.org/10.1039/d0cc04122jDOI Listing
August 2020

Melatonin Ameliorates MI-Induced Cardiac Remodeling and Apoptosis through a JNK/p53-Dependent Mechanism in Diabetes Mellitus.

Oxid Med Cell Longev 2020 9;2020:1535201. Epub 2020 Jan 9.

Department of Cardiovascular Surgery, Xijing Hospital, The Air Force Medical University, 710032, China.

Diabetes mellitus, a worldwide health threat, is considered an independent risk factor for cardiovascular diseases. The overall cardiovascular risk of diabetes is similar to the one having one myocardial infarction (MI) attack although the precise impact of diabetes on MI-induced myocardial anomalies remains elusive. Given that mortality following MI is much greater in diabetic patients compared to nondiabetic patients, this study was designed to examine the effect of melatonin on MI injury-induced myocardial dysfunction in diabetes. Adult mice were made diabetic using high-fat feeding and streptozotocin (100 mg/kg body weight) prior to MI and were treated with melatonin (50 mg/kg/d, p.o.) for 4 weeks prior to assessment of cardiac geometry and function. The MI procedure in diabetes displayed overt changes in cardiac geometry (chamber dilation and interstitial fibrosis) and functional anomalies (reduced fractional shortening and cardiomyocyte contractile capacity) in association with elevated c-Jun N-terminal kinase (JNK) phosphorylation and p53 level. Melatonin treatment markedly attenuated cardiac dysfunction and myocardial fibrosis in post-MI diabetic mice. Furthermore, melatonin decreased JNK phosphorylation, reduced p53 levels, and suppressed apoptosis in hearts from the post-MI diabetic group. findings revealed that melatonin effectively counteracted high-glucose/high fat-hypoxia-induced cardiomyocyte apoptosis and contractile dysfunction through a JNK-mediated mechanism, the effects of which were impaired by the JNK activator anisomycin. In summary, our study suggests that melatonin protects against myocardial injury in post-MI mice with diabetes, which offers a new therapeutic strategy for the management of MI-induced cardiac injury in diabetes.
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http://dx.doi.org/10.1155/2020/1535201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7199622PMC
January 2021

Melatonin protects against thoracic aortic aneurysm and dissection through SIRT1-dependent regulation of oxidative stress and vascular smooth muscle cell loss.

J Pineal Res 2020 Aug 27;69(1):e12661. Epub 2020 May 27.

Department of Cardiovascular Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, China.

Melatonin functions as an endogenous protective molecule in multiple vascular diseases, whereas its effects on thoracic aortic aneurysm and dissection (TAAD) and underlying mechanisms have not been reported. In this study, TAAD mouse model was successfully induced by β-aminopropionitrile fumarate (BAPN). We found that melatonin treatment remarkably prevented the deterioration of TAAD, evidenced by decreased incidence, ameliorated aneurysmal dilation and vascular stiffness, improved aortic morphology, and inhibited elastin degradation, macrophage infiltration, and matrix metalloproteinase expression. Moreover, melatonin blunted oxidative stress damage and vascular smooth muscle cell (VSMC) loss. Notably, BAPN induced a decrease in SIRT1 expression and activity of mouse aorta, whereas melatonin treatment reversed it. Further mechanistic study demonstrated that blocking SIRT1 signaling partially inhibited these beneficial effects of melatonin on TAAD. Additionally, the melatonin receptor was involved in this phenomenon. Our study is the first to report that melatonin exerts therapeutic effects against TAAD by reducing oxidative stress and VSMC loss via activation of SIRT1 signaling in a receptor-dependent manner, thus suggesting a novel therapeutic strategy for TAAD.
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http://dx.doi.org/10.1111/jpi.12661DOI Listing
August 2020

Evaluation of the auxiliary diagnostic value of antibody assays for the detection of novel coronavirus (SARS-CoV-2).

J Med Virol 2020 10 11;92(10):1975-1979. Epub 2020 Jul 11.

Department of Respiratory, the Second People's Hospital of Fuyang, Fuyang, China.

The spread of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has taken on pandemic proportions, affecting over 100 countries in a matter of weeks. The goal of this study was to assess the diagnostic values of different methods of detecting and estimating the SARS-CoV-2 infection, and the auxiliary diagnostic potential of antibody assays. By retrospectively analyzing the data of viral RNAs and serum immunoglobulin M-immunoglobulin G antibodies against SARS-CoV-2 from 38 cases with confirmed coronavirus disease 2019 in the Second People's Hospital of Fuyang, we found that, in the early phase of the illness, the viral RNA was most abundant in the sputum specimens, followed by that in the throat swabs, while the antibody assays identified fewer positive cases at this stage. However, the sensitivity of the antibody assays overtook that of RNA test from the eighth day of disease onset. Simultaneous use of antibody assay and reverse transcription-quantitative real-time polymerase chain reaction improved the sensitivity of the diagnoses. Moreover, we found that most of these cases with no detectable viral RNA load during the early stages were able to be seropositive after 7 days. Our findings indicate that the antibody detection could be used as an effective supplementary indicator of SARS-CoV-2 infection in suspected cases with no detectable viral RNA, and in conjunction with nucleic acid detection in confirming the infection.
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http://dx.doi.org/10.1002/jmv.25919DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7264661PMC
October 2020

Diagnostic utility of clinical laboratory data determinations for patients with the severe COVID-19.

J Med Virol 2020 07 10;92(7):791-796. Epub 2020 Apr 10.

Department of Microbiology, Anhui Medical University, Hefei, Anhui, China.

The role of clinical laboratory data in the differential diagnosis of the severe forms of COVID-19 has not been definitely established. The aim of this study was to look for the warning index in severe COVID-19 patients. We investigated 43 adult patients with COVID-19. The patients were classified into mild group (28 patients) and severe group (15 patients). A comparison of the hematological parameters between the mild and severe groups showed significant differences in interleukin-6 (IL-6), d-dimer (d-D), glucose, thrombin time, fibrinogen, and C-reactive protein (P < .05). The optimal threshold and area under the receiver operator characteristic curve (ROC) of IL-6 were 24.3 and 0.795 µg/L, respectively, while those of d-D were 0.28 and 0.750 µg/L, respectively. The area under the ROC curve of IL-6 combined with d-D was 0.840. The specificity of predicting the severity of COVID-19 during IL-6 and d-D tandem testing was up to 93.3%, while the sensitivity of IL-6 and d-D by parallel test in the severe COVID-19 was 96.4%. IL-6 and d-D were closely related to the occurrence of severe COVID-19 in the adult patients, and their combined detection had the highest specificity and sensitivity for early prediction of the severity of COVID-19 patients, which has important clinical value.
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http://dx.doi.org/10.1002/jmv.25770DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7228247PMC
July 2020

Use of the inferior whorl to detecting age-related changes in human corneal subbasal nerve plexus with laser-scanning confocal microscopy.

Ophthalmic Res 2020 Mar 5. Epub 2020 Mar 5.

Purpose: To determine the effect of aging on the corneal subbasal nerve plexus (SNP) by employing a wide-field mapping technique of composite images, scanned at the location of a distinctive spiraled subbasal nerve pattern located 1 to 2 mm inferior to the corneal apex (the inferior whorl) for SNP structural quantification.

Material And Methods: The central corneal tactile sensitivity (CCTS) and inferior whorl length (IWL) were compared among individuals in three age groups (20-39 years, 40-59 years, and 60-79 years). Statistical analyses constituted the Kruskal-Wallis test, one-way analysis of variance (with post hoc least significant difference test), Spearman correlation coefficient, and linear regression analysis.

Results: CCTS remained stable until the age of 50 years, when it began to decrease; the mean CCTS was 58.15±2.46 mm in the group aged 20-39, 55.74±3.85 mm in the group aged 40-59, and 50.23±3.27 mm in the group aged 60-79. IWL decreased with increasing age, with a corresponding linear decline of 0.2088 mm/mm2 per year, and the mean IWL was 25.43±4.50 mm/mm2 in the group aged 20-39, 22.71±6.19 mm/mm2 in the group aged 40-59, and 18.60±4.21 mm/mm2 in the group aged 60-79.

Conclusion: Our work provided a more accurate and repeatable method for corneal nerve analysis using Laser-Scanning Confocal Microscopy (LSCM). By using this technique, we confirmed that aging is associated with progressive reduction in subbasal nerve length.
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http://dx.doi.org/10.1159/000506952DOI Listing
March 2020

QTL-Seq and Sequence Assembly Rapidly Mapped the Gene BrMYBL2.1 for the Purple Trait in Brassica rapa.

Sci Rep 2020 02 11;10(1):2328. Epub 2020 Feb 11.

Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.

Anthocyanins have strong antioxidant activity and are believed to be healthy for human beings. The Brassica rapa L. ssp. chinensis var. purpurea "Zicaitai" is rich in anthocyanins. We constructed an F population of Zicaitai and "Caixin" (Brassica rapa ssp. parachinensis) and it shows clear segregation of the purple phenotype (i.e., variation in anthocyanin enrichment). Here, quantitative trait locus (QTL)-Seq was performed with two sample groups from the F population: one exhibiting an intense purple phenotype and the other showed a completely green phenotype. The results showed that the QTL-Seq and linkage analysis located different major loci. This indicates that there are two major genetic factors that plays different roles in regulating anthocyanin enrichment in Zicaitai. This was further supported by the data simulation of an in silico F population that QTL-Seq and linkage analysis can locate different major loci. Furthermore, the draft genomes of the two parents (Zicaitai and Caixin) were assembled and utilized to search for mutations in candidate genes. A ~100-bp insertion was found in the third exon of gene BrMYBL2.1 in Zicaitai. BrMYBL2.1 is a negative regulator of anthocyanin biosynthesis, while BrEGL3.2-previously located by linkage mapping-is a positive regulator. For these populations with multiple genes contributing large effects to a trait, a strategy of low depth re-sequencing of F individuals followed by QTL-Seq analysis with the free combination of sample groups is proposed. Furthermore, draft-sequence assembly of parental genomes together with QTL mapping is suggested as an efficient means for fine-mapping genes rapidly in segregating populations.
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http://dx.doi.org/10.1038/s41598-020-58916-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012920PMC
February 2020

Variation in the BrHMA3 coding region controls natural variation in cadmium accumulation in Brassica rapa vegetables.

J Exp Bot 2019 10;70(20):5865-5878

State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China.

Brassica rapa includes several important leafy vegetable crops with the potential for high cadmium (Cd) accumulation, posing a risk to human health. This study aims to understand the genetic basis underlying the variation in Cd accumulation among B. rapa vegetables. Cd uptake and translocation in 64 B. rapa accessions were compared. The role of the heavy metal ATPase gene BrHMA3 in the variation of Cd accumulation was investigated. BrHMA3 encodes a tonoplast-localized Cd transporter. Five full-length and four truncated haplotypes of the BrHMA3 coding sequence were identified, explaining >80% of the variation in the Cd root to shoot translocation among the 64 accessions and in F2 progeny. Truncated BrHMA3 haplotypes had a 2.3 and 9.3 times higher shoot Cd concentration and Cd translocation ratio, respectively, than full-length haplotypes. When expressed in yeast and Arabidopsis thaliana, full-length BrHMA3 showed activity consistent with a Cd transport function, whereas truncated BrHMA3 did not. Variation in the BrHMA3 promoter sequence had little effect on Cd translocation. Variation in the BrHMA3 coding sequence is a key determinant of Cd translocation to and accumulation in the leaves of B. rapa. Strong alleles of BrHMA3 can be used to breed for B. rapa vegetables that are low in Cd in their edible portions.
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http://dx.doi.org/10.1093/jxb/erz310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6812716PMC
October 2019

C1q/tumor necrosis factor-related protein-3-engineered mesenchymal stromal cells attenuate cardiac impairment in mice with myocardial infarction.

Cell Death Dis 2019 07 11;10(7):530. Epub 2019 Jul 11.

Department of Geriatric, Xijing Hospital, the Fourth Military Medical University, 710032, Xi'an, China.

Mesenchymal stromal cells (MSCs) transplantation offers an attractive alternative in myocardial infarctive therapy. However, poor cell engraftment and survival limit their restorative capacity. C1q/tumor necrosis factor-related protein-3 (CTRP3) inhibits reverse remodeling after myocardial infarction (MI) and was found to be secreted by MSCs in our preliminary experiments. We examined whether the overexpression of CTRP3 improved the survival of transplanted MSCs and augmented their efficacy on MI and whether silencing CTRP3 attenuated these effects. For gain-of-function analysis, MSCs overexpressing CTRP3 (LvC3-MSCs), control virus-transfected MSCs (LvNull-MSCs), MSCs alone, or phosphate-buffered saline (PBS) were injected into the peripheral areas of the infarction immediately after coronary artery ligation. For loss-of-function analysis, mice subjected to MI were randomized into groups and administered CTRP3-knockdown MSCs (LvshC3-MSCs), Lvshctrl-MSCs, MSCs, or PBS. Survival rates, cardiac function, and myocardial remodeling in mice were evaluated after 4 weeks. Injection of MSCs or LvNull-MSCs improved the left ventricular ejection fraction, inhibited cardiac fibrosis, and regulated cellular profiles of the infarction border zone 4 weeks after MI compared with those in the PBS group. Furthermore, overexpression of hCTRP3 promoted the efficacy of MSCs in the treatment of MI. However, knocking down CTRP3 impaired that. Coculture experiments confirmed that hCTRP3-enriched conditioned medium (CM) promoted MSCs migration and protected against HO-induced cell damage. Conversely, CM from C3 MSCs (CTRP3 knock out) significantly reduced the migration and antioxidative effects of MSCs. CTRP3 protein alone promoted MSCs proliferation and migration by upregulating matrix metalloproteinase 9 (MMP9) and protecting against oxidation by increasing superoxide dismutase 2 (SOD2) and metallothionein 1/2 (MT1/2) expression; and these effects were blocked by pretreatment with the extracellular signal-regulated kinase (ERK1/2) inhibitor U0126. Overexpression of CTRP3 significantly improved the MSCs-based efficacy on MI by increasing cell survival and retention via a mechanism involving ERK1/2-MMP9 and ERK1/2-SOD2/MT1/2 signaling.
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http://dx.doi.org/10.1038/s41419-019-1760-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6624206PMC
July 2019

C1q-TNF-related protein-3 attenuates pressure overload-induced cardiac hypertrophy by suppressing the p38/CREB pathway and p38-induced ER stress.

Cell Death Dis 2019 07 8;10(7):520. Epub 2019 Jul 8.

Department of Cardiovascular Surgery, Xijing Hospital, The Fourth Military Medical University, 127 Changle West Road, 710032, Xi'an, China.

C1q-tumor necrosis factor-related protein-3 (CTRP3) is an adipokine, which exerts protective function in ischemic or diabetic heart injury. However, the role of CTRP3 in cardiac hypertrophy remains unclear. The aim of this study was to investigate the pharmacological effects of CTRP3 on pathological cardiac hypertrophy induced by hypertension. Male C57BL/6 J wild-type (WT) mice, Ctrp3 knockout mice, and mice infected with lentivirus overexpressing mouse Ctrp3 underwent sham surgery or transverse aortic constriction (TAC) surgery. After 4 weeks, cardiac hypertrophy, fibrosis, and cardiac function were examined. Compared with WT mice, Ctrp3 deficiency substantially impaired contractile dysfunction, exacerbated the enlargement of cardiomyocytes and myocardial fibrosis, and reprogramed the expression of pathological genes after TAC. Conversely, CTRP3 overexpression played a role in restoring the left ventricular cardiac contractile function, alleviating cardiac hypertrophy and fibrosis, and inhibiting the expression of hypertrophic and fibrotic signaling in mice after TAC. Furthermore, CTRP3 regulated the expression of the p38/CREB pathway and of the primary modulating factors of the endoplasmic reticulum stress, i.e., GRP78 and the downstream molecules eukaryotic translation inhibition factor 2 submit α, C/EBP homologous protein, and inositol-requiring enzyme-1. Further, inhibition of p38 MAPK by SB203580 blunted the ER stress intensified by Ctrp3 deficiency. In vitro, CTRP3 protected neonatal rat cardiac myocytes against phenylephrine-induced cardiomyocyte hypertrophy. We conclude that CTRP3 protects the host against pathological cardiac remodeling and left ventricular dysfunction induced by pressure overload largely by inhibiting the p38/CREB pathway and alleviating p38-induced ER stress.
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http://dx.doi.org/10.1038/s41419-019-1749-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6614451PMC
July 2019

Synthesis and characterization of aminopyridine iron(ii) chloride catalysts for isoprene polymerization: sterically controlled monomer enchainment.

Dalton Trans 2019 Jun 10;48(22):7862-7874. Epub 2019 May 10.

Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.

In this study, a series of 2-R-6-(1-(alkylamino)methyl)pyridine-iron complexes [alkyl: (CPh) Fe1; (CHPh) Fe2; (CHPh) Fe3; (CHMePh) Fe4; (CHPh) Fe5; (CHMe) Fe6; (CH) Fe7; (CH(4-OMe)Ph) Fe8; (CH(4-CF)Ph) Fe9; (CH(2,4,6-Me)Ph) Fe10; (CHPh) Fe11] were synthesized and well characterized by ATR-IR spectroscopy, HRMS spectroscopy and elemental analysis. In addition, Fe3, Fe4, Fe7 and Fe11 were characterized by X-ray diffraction analysis: Fe3 and Fe11 adopted distorted tetrahedral geometries in the solid state while Fe4 and Fe7 were found in dimeric or polymeric forms respectively in which chlorides acted as bridging ligands. The catalytic capacities of these iron complexes were investigated for isoprene polymerization. Upon activation with a MAO cocatalyst, the catalytic activities of complexes varied as a function of the steric and electronic influences of substituents. In general, the catalysts bearing the least steric groups and electron-withdrawing groups exhibited relatively high activities. An outstanding activity of 190.6 × 10 g·mol·h was obtained by Fe5 [CHPh]. Moreover, changes in the steric hindrance around the metal center showed a notable effect on the selectivity of monomer enchainment. In particular, most of the polymers obtained by these complexes bearing flexible frameworks were in favor of 3,4-enchainment.
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http://dx.doi.org/10.1039/c9dt00452aDOI Listing
June 2019

Influences of Fluorine Substituents on Iminopyridine Fe(II)- and Co(II)-Catalyzed Isoprene Polymerization.

Polymers (Basel) 2018 Aug 22;10(9). Epub 2018 Aug 22.

Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.

A series of iminopyridine complexes of Fe(II) and Co(II) complexes bearing fluorinated aryl substituents were synthesized for the polymerization of isoprene. The structures of complexes , and were determined by X-ray diffraction analysis. Complex contained two iminopyridine ligands coordinated to the iron metal center forming an octahedral geometry, whereas adopted a chloro-bridged dimer, and featured with two patterns of cobalt centers bridged via chlorine atoms. Complexes and represented rare examples of chlorine bridged bimetallic Co(II) complexes. The fluorine substituents effects, particularly on catalytic activity and polymer properties such as molecular weight and regio-/stereo-selectivity were investigated when these complexes were employed for isoprene polymerization. Among the Fe(II)/methylaluminoxane (MAO) systems, the 4-CF₃ substituted iminopyridine Fe(II) complex was found as a highly active isoprene polymerization catalyst exhibiting the highest activity of 10⁶ g·(mol of Fe)·h. The resultant polymer displayed lower molecular weight ( = 3.5 × 10⁴ g/mol) and moderate polydispersity index (PDI = 2.1). Furthermore, the ratio of -1,4-/3,4 was not affected by the F substituents. In the series of Co(II)/AlEt₂Cl binary systems, complexes containing electron-withdrawing N-aryl substituents (R = 4-CF₃, 2,6-2F) afforded higher molecular weights polyisoprene than that was obtained by the complex containing electron-donating N-alkyl substituents (R = octyl). However, ternary components system, complex/MAO/[Ph₃C][B(C₆F₅)₄] resulted in low molecular weight polyisoprene ( < 2000) with high -1,4-unit (>95%).
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http://dx.doi.org/10.3390/polym10090934DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6403809PMC
August 2018

GPR 30 reduces myocardial infarct area and fibrosis in female ovariectomized mice by activating the PI3K/AKT pathway.

Life Sci 2019 Jun 21;226:22-32. Epub 2019 Mar 21.

Cardiovascular Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, PR China. Electronic address:

Aims: Estrogen plays an important role in cardioprotection. Animal experiments showed that the G-protein coupled estrogen receptor 30 (GPR30) specific agonist G1 could reduce post-ischemic dysfunction and inhibit cardiac fibroblast proliferation. However, the underlying mechanism of action is not clear. The current study tests the hypothesis that GPR30 reduces myocardial infarct area and fibrosis in female ovariectomized (OVX) mice by activating the PI3K/AKT pathway.

Main Methods: In this study, we established a myocardial infarction (MI) animal model derived from OVX C57BL/6 female mice, and investigated the effect of G1 on cardiac function by echocardiography and Hemodynamics, morphology and expression of fibrosis-related and apoptosis-related proteins by Masson's trichrome and H&E, Immunofluorescence, Western blotting and TUNEL.

Key Findings: Combination with OVX significantly increased myocardial fibrosis and MI area compared to MI treatment alone, as determined by echocardiography and hemodynamics. Further addition of G1 changed the expression of apoptosis-related proteins, decreased the levels of tumor necrosis factor-α and interleukin-10, and reduced the degree of myocardial fibrosis and myocardial infarct area. Primary cultured cardiac fibroblasts (CFs) were subjected to hypoxia/serum deprivation (H/SD) simulating the in vivo ischemia model. When the PI3K/AKT pathway was inhibited by wortmanin in H/SD CFs, G1 failed to induce significant changes in the expression of apoptosis-related proteins.

Significance: It suggested that GPR30 may improve cardiac function in female OVX mice by activating the PI3K/AKT pathway and reducing myocardial infarct size and fibrosis.
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http://dx.doi.org/10.1016/j.lfs.2019.03.049DOI Listing
June 2019

Whole-genome resequencing reveals Brassica napus origin and genetic loci involved in its improvement.

Nat Commun 2019 03 11;10(1):1154. Epub 2019 Mar 11.

College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China.

Brassica napus (2n = 4x = 38, AACC) is an important allopolyploid crop derived from interspecific crosses between Brassica rapa (2n = 2x = 20, AA) and Brassica oleracea (2n = 2x = 18, CC). However, no truly wild B. napus populations are known; its origin and improvement processes remain unclear. Here, we resequence 588 B. napus accessions. We uncover that the A subgenome may evolve from the ancestor of European turnip and the C subgenome may evolve from the common ancestor of kohlrabi, cauliflower, broccoli, and Chinese kale. Additionally, winter oilseed may be the original form of B. napus. Subgenome-specific selection of defense-response genes has contributed to environmental adaptation after formation of the species, whereas asymmetrical subgenomic selection has led to ecotype change. By integrating genome-wide association studies, selection signals, and transcriptome analyses, we identify genes associated with improved stress tolerance, oil content, seed quality, and ecotype improvement. They are candidates for further functional characterization and genetic improvement of B. napus.
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http://dx.doi.org/10.1038/s41467-019-09134-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6411957PMC
March 2019

A naturally occurring variation in the gene is associated with aliphatic glucosinolate accumulation in leaves.

Hortic Res 2018 1;5:69. Epub 2018 Dec 1.

1Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081 Beijing, China.

Glucosinolate profiles significantly vary among genotypes. However, the molecular basis of these variations is largely unknown. In this study, we investigated a major quantitative trait locus (QTL) controlling aliphatic glucosinolate accumulation in leaves. The QTL, which encompasses three tandem genes and two genes, was detected in two BCDH populations. Among the five-candidate genes, only the expression level of (Bra013007) was significantly correlated with the accumulation of aliphatic glucosinolates in leaves. We identified a naturally occurring insertion within exon 1 of , which is predicted to be a loss-of-function mutation, as confirmed by qRT-PCR. We determined that the loss of function was associated with the low glucosinolate content in accessions. Furthermore, overexpressing the gene resulted in an increase in total aliphatic glucosinolates in transgenic lines. Our study provides insights into the molecular mechanism underlying the accumulation of aliphatic glucosinolates in leaves, thereby facilitating in the manipulation of total aliphatic glucosinolate content in crops.
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http://dx.doi.org/10.1038/s41438-018-0074-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6269504PMC
December 2018

High-performance solar-blind SnO nanowire photodetectors assembled using optical tweezers.

Nanoscale 2019 Jan;11(5):2162-2169

Hunan Key Laboratory for Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha, Hunan 410083, P. R. China.

One-dimensional semiconducting SnO2 nanowires with wide bandgaps are promising candidates to build many important optoelectronic devices. Because building these devices involves the assembly of nanowires into complex structures, manipulation of the active materials needs to be done with high spatial precision. In this paper, an optical tweezer system, comprising a spatial light-modulator, a microscope, and optical elements, is used to individually trap, transfer, and assemble SnO2 nanowires into two-terminal photodetectors in a liquid environment. After the assembly using optical trapping, the two ends of the SnO2 nanowire photodetectors, which are connected with the electrodes, were further stabilized using a focused laser. During exposure to 275 nm deep-ultraviolet light, the as-assembled photodetectors show a high Iph/Idark ratio of 2.99 × 105, a large responsivity of 4.3 × 104 A W-1, an excellent external quantum efficiency of 1.94 × 105, and a high detectivity of 2.32 × 1013 Jones. The photoresponse-speed of the devices could be improved further using passivation with a polymer. The rise and decay times are about 60 ms and 100 ms, respectively. As a result of this study, we can confirm that non-contact optical trapping can enable the construction of nanowire architectures for optoelectronic, bioelectronic, and other devices.
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http://dx.doi.org/10.1039/c8nr07382aDOI Listing
January 2019

Reply to: 'Organization of the genome sequence of the polyploid crop species Brassica juncea'.

Nat Genet 2018 11;50(11):1497-1498

Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China.

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http://dx.doi.org/10.1038/s41588-018-0240-7DOI Listing
November 2018

Author Correction: The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection.

Nat Genet 2018 11;50(11):1616

Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China.

Following publication of this article, the authors have corrected 426 chimeric scaffolds in this genome (total scaffold number 10,684). The genome assembly has now been improved as V1.5, and the updated genome assembly is available to be downloaded from http://brassicadb.org/brad/datasets/pub/Genomes/Brassica_juncea/V1.5/ .
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http://dx.doi.org/10.1038/s41588-018-0227-4DOI Listing
November 2018

Fine mapping and candidate gene screening of the downy mildew resistance gene RPF1 in Spinach.

Theor Appl Genet 2018 Dec 22;131(12):2529-2541. Epub 2018 Sep 22.

Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.

Key Message: A SLAF-BSA approach was used to locate the RPF1 locus. The three most likely candidate genes were identified which provide a basic for cloning the resistance gene at the RPF1 locus. Spinach downy mildew is a globally devastating oomycete disease. The use of downy mildew resistance genes constitutes the most effective approach for disease management. Hence, the objective of the present study was to fine map the first-reported resistance locus RPF1. The resistance allele at this resistance locus was effective against races 1-7, 9, 11, 13, and 15 of Peronospora farinosa f. sp. spinaciae (P. effusa). The approach fine mapped RPF1 using specific-locus amplified fragment sequencing (SLAF-Seq) technology combined with bulked segregant analysis. A 1.72 Mb region localized on chromosome 3 was found to contain RPF1 based on association analysis. After screening recombinants with the SLAF markers within the region, the region was narrowed down to 0.89 Mb. Within this region, 14 R genes were identified based on the annotation information. To identify the genes involved in resistance, resequencing of two resistant inbred lines (12S2 and 12S3) and three susceptible inbred lines (12S1, 12S4, and 10S2) was performed. The three most likely candidate genes were identified via amino acid sequence analysis and conserved domain analysis between resistant and susceptible inbred lines. These included Spo12729, encoding a receptor-like protein, and Spo12784 and Spo12903, encoding a nucleotide-binding site and leucine-rich repeat domains. Additionally, based on the sequence variation in the three genes between the resistant and susceptible lines, molecular markers were developed for marker-assisted selection. The results could be valuable in cloning the RPF1 alleles and improving our understanding of the interaction between the host and pathogen.
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http://dx.doi.org/10.1007/s00122-018-3169-4DOI Listing
December 2018

GPR30 Attenuates Myocardial Fibrosis in Diabetic Ovariectomized Female Rats: Role of iNOS Signaling.

DNA Cell Biol 2018 Oct 18;37(10):821-830. Epub 2018 Sep 18.

1 Department of Cardiovascular Surgery, Xijing Hospital, The Fourth Military Medical University , Xi'an, Shaanxi, China .

Premenopausal women have a reduced risk for cardiovascular disease. Estrogen deficiency augments cardiac inflammation and oxidative stress and, thereby, aggravates myocardial fibrosis (MF) and diastolic dysfunction in hypertensive female rats. However, estrogen replacement therapy has no effect on myocardial infarction and cardiac fibrosis in postmenopausal women. Further clinical studies showed that high blood glucose levels in patients with diabetes is an important cause of MF, but the underlying mechanism is unclear. To experimentally address this issue, diabetes mellitus (DM) was induced by injecting streptozotocin and administering a high-fat diet in ovariectomized (OVX) rats. High degrees of fibrosis and apoptosis were detected in the cardiac tissue of these rats, together with increased expression of iNOS. Further treatment with the G protein-coupled estrogen receptor 30 (GPR30) agonist G1 decreased iNOS expression and the apoptosis rate in cardiac tissue significantly and inhibited cardiac fibroblast (CF) proliferation. Similar trends were observed in cultured CFs treated with high concentrations of fat and glucose. In addition, treatment with the iNOS-specific inhibitor W1400 attenuated iNOS and vimentin expression, which is associated with a marked reduction in MF. These results suggest that GPR30 activation inhibits MF in diabetic OVX female rats by suppressing cardiac iNOS activity and consequently NO levels. Thus, GPR30 activation may provide novel cardioprotection strategies for postmenopausal women, especially those with DM.
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http://dx.doi.org/10.1089/dna.2018.4208DOI Listing
October 2018
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