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Wang X, Zhang X, Fan D, Gong J, Li S, Gao Y, Liu A, Liu L, Deng X, Shi Y, Shang H, Zhang Y, Yuan Y. AAQSP increases mapping resolution of stable QTLs through applying NGS-BSA in multiple genetic backgrounds. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3223-3235. [PMID: 35904626 DOI: 10.1007/s00122-022-04181-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
In this study, we present AAQSP as an extension of existing NGS-BSA applications for identifying stable QTLs at high resolution. GhPAP16 and GhIQD14 fine mapped on chromosome D09 of upland cotton are identified as important candidate genes for lint percentage (LP). Bulked segregant analysis combined with next generation sequencing (NGS-BSA) allows rapid identification of genome sequence differences responsible for phenotypic variation. The NGS-BSA approach applied to crops mainly depends on comparing two bulked DNA samples of individuals from an F2 population. Since some F2 individuals still maintain high heterozygosity, heterosis will exert complications in pursuing NGS-BSA in such populations. In addition, the genetic background influences the stability of gene expression in crops, so some QTLs mapped in one segregating population may not be widely applied in crop improvement. The AAQSP (Association Analysis of QTL-seq on Semi-homologous Populations) reported in our study combines the optimized scheme of constructing BSA bulks with NGS-BSA analysis in two (or more) different parental genetic backgrounds for isolating the stable QTLs. With application of AAQSP strategy and construction of a high-density linkage map, we have successfully identified a QTL significantly related to lint percentage (LP) in cultivated upland cotton, followed by map-based cloning to dissect two candidate genes, GhPAP16 and GhIQD14. This study demonstrated that AAQSP can efficiently identify stable QTLs for complex traits of interest, and thus accelerate the genetic improvement of upland cotton and other crop plants.
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Geng Y, Song Z, Zhang X, Deng X, Wang Y, Zhang Z. POS0315 DIAGNOSTIC PERFORMANCE OF CASPAR CRITERIA FOR PSORIATIC ARTHRITIS WITH OR WITHOUT INTEGRATION OF ULTRASOUND. Ann Rheum Dis 2022. [DOI: 10.1136/annrheumdis-2022-eular.3605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BackgroundAlthough the CASPAR criteria in the diagnosis of psoriatic arthritis (PsA) have been validated, CASPAR based on physical examination (PE) is not “gold standard”. The ultrasound (US) could improve the diagnostic accuracy as compared to clinical examination alone.ObjectivesTo evaluate the diagnostic performance of CASPAR criteria for psoriatic arthritis (PsA) with or without integration of ultrasound (US).MethodsThe patients with hint of PsA were enrolled. Tender and swollen joint counts, presents of enthesitis and dactylitis were collected by physical examination (PE). US was performed to evaluate peripheral joints, entheses and tendons. The additional value of US to CASPAR criteria were analysed.Results326 consecutive patients were enrolled, with 164 PsA and 162 non-PsA. Significantly higher frequencies of tenosynovitis and enthesitis on US and new bone formation on X-ray were found in PsA than non-PsA patients (56.7% vs. 13.0%; 62.2% vs. 14.2%; 62.2% vs. 8.0%, p<0.01 for all). Logistic regression analysis showed that dactylitis (OR=12.0, p<0.01), family history of PsO/PsA (OR=3.1, p<0.05), nail involvement (OR=3.5, p=0.01), new bone formation (OR=14.8, p<0.01) and tenosynovitis on US (OR=21.3, p<0.01), enthesitis on US (OR=21.7, p<0.01) were independent risk factors for PsA. Adding US tenosynovitis and/or enthesitis to CASPAR criteria showed better performance by improving the specificity (91.4% vs. 67.9%) and meanwhile keeping sensitivity (92.1% vs. 96.3%). When replacing hand X-ray by US in CASPAR criteria, the sensitivity and specificity were comparable to CASPAR criteria adding with US. The diagnostic accuracy was 82.2% for CASPAR criteria based on PE, 91.7% for CASPAR integrated with US, and 91.4% for CASPAR with US to replace X-ray.ConclusionCASPAR criteria based on US improve the diagnosis utility of PsA than CASPAR criteria based on PE. US assessment is valuable in the diagnosis of PsA.References[1]Fiorenza A, Bonitta G, Gerratana E, et al. Assessment of enthesis in patients with psoriatic arthritis and fibromyalgia using clinical examination and ultrasound. Clinical and experimental rheumatology 2020;38 Suppl 123:31-9.[2]Zabotti A, Bandinelli F, Batticciotto A, et al. Musculoskeletal ultrasonography for psoriatic arthritis and psoriasis patients: a systematic literature review. Rheumatology (Oxford) 2017;56:1518-32.Figure 1.ROC curves for adding US or substituting X-ray by US in CASPAR criteria. Receiver operating characteristic (ROC) curve illustrates the diagnosis performance of CASPAR criteria adding US or substituting X-ray by US in CASPAR criteria and CASPAR criteria based on PE alone. The area under the curve of the ROC curve (AUC) was 0.929 (95%CI 0.897, 0.961) (p<0.01) for adding US to CASPAR criteria. AUC was 0.908 (95%CI 0.876, 0.940) (p<0.01) for CASPAR criteria based on PE. And AUC was 0.916 (95%CI 0.880, 0.951) (p<0.01) for substituting X-ray by US in CASPAR criteria. CASPAR: ClASsification criteria for Psoriatic ARthritis; PE: physical examination; US: ultrasound.Disclosure of InterestsNone declared
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Deng X, He HQ, Zhou Y, Yan R, Tang XW, Zhu Y, Xu XP, Lyu HK. [Advances in research of interchangeable immunization with live attenuated Japanese encephalitis vaccines and inactivated vaccines]. ZHONGHUA YU FANG YI XUE ZA ZHI [CHINESE JOURNAL OF PREVENTIVE MEDICINE] 2022; 56:554-560. [PMID: 35644967 DOI: 10.3760/cma.j.cn112150-20211110-01044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Japanese encephalitis (JE) virus is the leading cause of vaccine-preventable encephalitis in Asia and the Western Pacific, which mainly invades central nervous system. Vaccination is the most important strategy to prevent JE. Currently, both live attenuated Japanese encephalitis vaccines (JE-L) and inactivated vaccines (JE-I) are in use. Due to the supply of vaccines and the personal choice of recipients, there will be a demand for interchangeable immunization of these two vaccines. However, relevant research is limited. By reviewing domestic and foreign research evidence, this article summarizes the current situation of the interchangeable use of JE-L and JE-I, and makes recommendations when the interchangeable immunization is in urgent need, so as to provide reference for practical vaccination and policymaking in China.
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Chen S, Peng Y, Liu Y, Zhao C, Deng X, Qin A, Yan D, Stevens C, Deraniyagala R, Ding X. PO-1503 MRI-based Synthetic CT images for IMPT Treatment Planning of Nasopharyngeal Carcinoma Patients. Radiother Oncol 2022. [DOI: 10.1016/s0167-8140(22)03467-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Jiang P, Qu A, Jiang W, Deng X, Wang J. PO-1340 Phase Ⅰ Trail of Concurrent Nab-paclitaxel and Cisplatin with VMAT for LACC. Radiother Oncol 2022. [DOI: 10.1016/s0167-8140(22)03304-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Pan J, Hu S, Ren X, Hu H, Deng X, Yu B, Cobos I, Chen X, Zhang W. Whole-Transcriptome Profiling and circRNA-miRNA-mRNA Regulatory Networks in B-Cell Development. Front Immunol 2022; 13:812924. [PMID: 35386709 PMCID: PMC8978327 DOI: 10.3389/fimmu.2022.812924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/11/2022] [Indexed: 11/13/2022] Open
Abstract
The generation and differentiation of B lymphocytes (B cells) is a flexible process with many critical regulatory factors. Previous studies indicated that non-coding RNAs play multiple roles in the development of lymphocytes. However, little has been known about the circular RNA (circRNA) profiles and their competing endogenous RNA (ceRNA) networks in B-cell development and differentiation. Here, four B-cell subsets were purified from single-cell suspensions of mouse bone marrow. Then RNA sequencing (RNA-Seq) was used to display expression profiles of circRNAs, miRNAs and mRNAs during B-cell differentiation. 175, 203, 219 and 207 circRNAs were specifically expressed in pro-B cells, pre-B cells, immature B cells and mature B cells, respectively. The circRNA-associated ceRNA networks constructed in two sequential stages of B-cell differentiation revealed the potential mechanism of circRNAs in these processes. This study is the first to explore circRNA profiles and circRNA-miRNA-mRNA networks in different B-cell developmental stages of mouse bone marrow, which contribute to further research on their mechanism in B-cell development and differentiation.
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Zhou Y, Tao MY, Lu ZJ, Yan R, Deng X, Tang XW, Zhu Y, He HQ, Yao YP. [Epidemiological characteristics and spatiotemporal clustering of hepatitis A in Zhejiang Province from 2010 to 2019]. ZHONGHUA YU FANG YI XUE ZA ZHI [CHINESE JOURNAL OF PREVENTIVE MEDICINE] 2022; 56:459-463. [PMID: 35488543 DOI: 10.3760/cma.j.cn112150-20210406-00330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Objective: To analyze the epidemiological characteristics and spatiotemporal clustering of hepatitis A in Zhejiang Province from 2010 to 2019. Methods: The data of hepatitis A incidence in Zhejiang Province from 2010 to 2019 were collected from the infectious disease surveillance system of China Information System for Disease Control and Prevention. ArcGIS 10.7 software was used for spatial autocorrelation analysis. SaTScan 9.6 software was used for spatiotemporal scanning analysis. SPSS 25.0 software was used for additional analysis. Results: Zhejiang Province has reported 5 465 cases of hepatitis A in 2010-2019 years, with an average annual incidence rate of 1.00/100 000, and periodicity and seasonality are not obvious. The incidence of male was higher than that of female (P=0.023), and the highest incidence rate was 50-59 years old. Spatial autocorrelation analysis showed that there was a positive spatial correlation between the incidence of hepatitis A in Zhejiang Province from 2010 to 2017, with the weakest correlation in 2010 (Moran's I =0.103, Z=1.769, P=0.049), and the strongest correlation in 2016 (Moran's I=0.328, Z=4.979, P=0.001). Spatiotemporal scanning analysis showed that there was spatial aggregation of hepatitis A in Zhejiang Province from 2010 to 2019, with a total of three aggregation areas identified. Among them, the mostly aggregation area was concentrated in Xiangshan county of Ningbo city, which covered 10 counties (cities and districts), including Ninghai county and Yinzhou district, and appeared from January 1 to June 30, 2012. Conclusion: The incidence level of hepatitis A in Zhejiang Province shows a stable fluctuation trend from 2010 to 2019, and the seasonal regularity is not obvious. The population group aged 50-59 years old is the key population. There is spatial aggregation in the epidemic situation of hepatitis A. Targeted prevention and control measures of hepatitis A should be done based on the law of spatiotemporal aggregation and local incidence.
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Han Z, Guo L, Yu X, Guo H, Deng X, Yu J, Deng X, Xu F, Zhang Z, Huang Y. Network-driven targeted analysis reveals that Astragali Radix alleviates doxorubicin-induced cardiotoxicity by maintaining fatty acid homeostasis. JOURNAL OF ETHNOPHARMACOLOGY 2022; 287:114967. [PMID: 34995692 DOI: 10.1016/j.jep.2022.114967] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/07/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Astragali Radix (AR) is a popular traditional Chinese medicine that has been used for more than 2000 years. It is a well-known tonic for weak people with chronic diseases, such as heart failure and cerebral ischemia. Previous studies have reported that AR could support the "weak heart" of cancer patients who suffered from doxorubicin (DOX)-induced cardiotoxicity (DIC). However, the underlying mechanism remains unclear. AIM OF THE STUDY This study aimed to uncover the critical pathways and molecular determinants for AR against DIC by fully characterizing the network-based relationship. MATERIALS AND METHODS We integrated ultra-high-performance liquid chromatography-high-resolution mass spectrometry (UHPLC-HRMS) profiling, database and literature searching, and the human protein-protein interactome to discover the specific network module associated with AR against DIC. To validate the network-based findings, a low-dose, long-term DIC mouse model and rat cardiomyoblast H9c2 cells were employed. The levels of potential key metabolites and proteins in hearts and cells were quantified by the LC-MS/MS targeted analysis and western blotting, respectively. RESULTS We constructed one of the most comprehensive AR component-target network described to date, which included 730 interactions connecting 64 unique components and 359 unique targets. Relying on the network-based evaluation, we identified fatty acid metabolism as a putative critical pathway and peroxisome proliferator-activated receptors (PPARα and PPARγ) as potential molecular determinants. We then confirmed that DOX caused the accumulation of fatty acids in the mouse failing heart, while AR promoted fatty acid metabolism and preserved heart function. By inhibiting PPARγ in H9c2 cells, we further found that AR could alleviate DIC by activating PPARγ to maintain fatty acid homeostasis. CONCLUSIONS Our findings imply that AR is a promising drug candidate that treats DIC by maintaining fatty acid homeostasis. More importantly, the network-based method developed here could facilitate the mechanism discovery of AR therapy and help catalyze innovation in its clinical application.
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Gong J, Peng Y, Yu J, Pei W, Zhang Z, Fan D, Liu L, Xiao X, Liu R, Lu Q, Li P, Shang H, Shi Y, Li J, Ge Q, Liu A, Deng X, Fan S, Pan J, Chen Q, Yuan Y, Gong W. Linkage and association analyses reveal that hub genes in energy-flow and lipid biosynthesis pathways form a cluster in upland cotton. Comput Struct Biotechnol J 2022; 20:1841-1859. [PMID: 35521543 PMCID: PMC9046884 DOI: 10.1016/j.csbj.2022.04.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 04/11/2022] [Accepted: 04/11/2022] [Indexed: 11/25/2022] Open
Abstract
Upland cotton is an important allotetraploid crop that provides both natural fiber for the textile industry and edible vegetable oil for the food or feed industry. To better understand the genetic mechanism that regulates the biosynthesis of storage oil in cottonseed, we identified the genes harbored in the major quantitative trait loci/nucleotides (QTLs/QTNs) of kernel oil content (KOC) in cottonseed via both multiple linkage analyses and genome-wide association studies (GWAS). In ‘CCRI70′ RILs, six stable QTLs were simultaneously identified by linkage analysis of CHIP and SLAF-seq strategies. In ‘0-153′ RILs, eight stable QTLs were detected by consensus linkage analysis integrating multiple strategies. In the natural panel, thirteen and eight loci were associated across multiple environments with two algorithms of GWAS. Within the confidence interval of a major common QTL on chromosome 3, six genes were identified as participating in the interaction network highly correlated with cottonseed KOC. Further observations of gene differential expression showed that four of the genes, LtnD, PGK, LPLAT1, and PAH2, formed hub genes and two of them, FER and RAV1, formed the key genes in the interaction network. Sequence variations in the coding regions of LtnD, FER, PGK, LPLAT1, and PAH2 genes may support their regulatory effects on oil accumulation in mature cottonseed. Taken together, clustering of the hub genes in the lipid biosynthesis interaction network provides new insights to understanding the mechanism of fatty acid biosynthesis and TAG assembly and to further genetic improvement projects for the KOC in cottonseeds.
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Razzaq A, Zafar MM, Ali A, Hafeez A, Sharif F, Guan X, Deng X, Pengtao L, Shi Y, Haroon M, Gong W, Ren M, Yuan Y. The Pivotal Role of Major Chromosomes of Sub-Genomes A and D in Fiber Quality Traits of Cotton. Front Genet 2022; 12:642595. [PMID: 35401652 PMCID: PMC8988190 DOI: 10.3389/fgene.2021.642595] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 10/25/2021] [Indexed: 02/02/2023] Open
Abstract
Lack of precise information about the candidate genes involved in a complex quantitative trait is a major obstacle in the cotton fiber quality improvement, and thus, overall genetic gain in conventional phenotypic selection is low. Recent molecular interventions and advancements in genome sequencing have led to the development of high-throughput molecular markers, quantitative trait locus (QTL) fine mapping, and single nucleotide polymorphisms (SNPs). These advanced tools have resolved the existing bottlenecks in trait-specific breeding. This review demonstrates the significance of chromosomes 3, 7, 9, 11, and 12 of sub-genomes A and D carrying candidate genes for fiber quality. However, chromosome 7 carrying SNPs for stable and potent QTLs related to fiber quality provides great insights for fiber quality-targeted research. This information can be validated by marker-assisted selection (MAS) and transgene in Arabidopsis and subsequently in cotton.
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Gong J, Kong D, Liu C, Li P, Liu P, Xiao X, Liu R, Lu Q, Shang H, Shi Y, Li J, Ge Q, Liu A, Deng X, Fan S, Pan J, Chen Q, Yuan Y, Gong W. Multi-environment Evaluations Across Ecological Regions Reveal That the Kernel Oil Content of Cottonseed Is Equally Determined by Genotype and Environment. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:2529-2544. [PMID: 35170322 DOI: 10.1021/acs.jafc.1c07082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cotton is the fifth-largest oil crop in the world. A high kernel oil content (KOC) and high stability are important cottonseed attributes for food security. In this study, the phenotype of KOC and the genotype-by-environment interaction factors were collectively dissected using 250 recombinant inbred lines, their parental cultivars sGK156 and 901-001, and CCRI70 across multi-environments. ANOVA and correlation analysis showed that both genotype and environment contributed significantly to KOC accumulation. Analyses of additive main effect multiplicative interaction and genotype-by-environment interaction biplot models presented the effects of genotype, environment, and genotype by environment on KOC performance and the stability of the experimental materials. Interaction network analysis revealed that meteorological and geographical factors explained 38% of the total KOC variance, with average daily rainfall contributing the largest positive impact and cumulative rainfall having the largest negative impact on KOC accumulation. This study provides insight into KOC accumulation and could direct selection strategies for improved KOC and field management of cottonseed in the future.
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Deng X, He HQ, Zhou Y, Yan R, Tang XW, Zhu Y, Xu XP, Lyu HK. [Evaluating the real-world vaccine effectiveness using a regression discontinuity design]. ZHONGHUA LIU XING BING XUE ZA ZHI = ZHONGHUA LIUXINGBINGXUE ZAZHI 2022; 43:292-296. [PMID: 35184499 DOI: 10.3760/cma.j.cn112338-20210706-00524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Estimating the actual real-world effectiveness of the vaccine is an essential part of the post-marketing evaluation. This regression discontinuity design (RDD) using observational data is designed to quantify the effect of an intervention when eligibility for the intervention is based on a defined cutoff as age, making it suited to estimate vaccine effects. This approach can avoid the high cost and ethical issues; overcome difficulties in the organization and practice process in randomized controlled trials, which leads to a higher level of causal inference evidence and more realistic results. Here, we describe key features of RDD in general, and then specific scenarios, with examples, to illustrate that RDD are an essential tool for advancing our understanding of vaccine effects.
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Xu Y, Deng X, Sun Y, Wang X, Xiao Y, Li Y, Chen Q, Jiang L. Optical Imaging in the Diagnosis of OPMDs Malignant Transformation. J Dent Res 2022; 101:749-758. [PMID: 35114846 DOI: 10.1177/00220345211072477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Oral potentially malignant disorders (OPMDs) are a heterogeneous group of oral lesions with a variable risk of malignant transformation to oral squamous cell carcinoma. The current OPMDs malignant transformation screening depends on conventional oral examination (COE) and is confirmed by biopsy and histologic examination. However, early malignant lesions with subtle mucosal changes are easily unnoticed by COE based on visual inspection and palpation. Optical techniques have been used to determine the biological structure, composition, and function of cells and tissues noninvasively by analyzing the changes in their optical properties. The oral epithelium and stroma undergo persistent structural, functional, and biochemical alterations during malignant transformation, leading to variations in optical tissue properties; optical techniques are thus powerful tools for detecting OPMDs malignant transformation. The optical imaging methods already used to detect OPMDs malignant transformation in vivo include autofluorescence imaging, narrowband imaging, confocal reflectance microscopy, and optical coherence tomography. They exhibit advantages over COE in detecting biochemical or morphologic changes at the molecular or cellular level in vivo; however, limitations also exist. This article comprehensively reviews the various real-time in vivo optical imaging methods used in the adjunctive diagnosis of OPMDs malignant transformation. We focus on the principles of these techniques, review their clinical application, and compare and summarize their advantages and disadvantages. Finally, we conclude with a discussion of current challenges and future directions of this field.
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Zhang Z, Gong J, Zhang Z, Gong W, Li J, Shi Y, Liu A, Ge Q, Pan J, Fan S, Deng X, Li S, Chen Q, Yuan Y, Shang H. Identification and analysis of oil candidate genes reveals the molecular basis of cottonseed oil accumulation in Gossypium hirsutum L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:449-460. [PMID: 34714356 DOI: 10.1007/s00122-021-03975-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/15/2021] [Indexed: 05/14/2023]
Abstract
Based on the integration of QTL-mapping and regulatory network analyses, five high-confidence stable QTL regions, six candidate genes and two microRNAs that potentially affect the cottonseed oil content were discovered. Cottonseed oil is increasingly becoming a promising target for edible oil with its high content of unsaturated fatty acids. In this study, a recombinant inbred line (RIL) cotton population was constructed to detect quantitative trait loci (QTLs) for the cottonseed oil content. A total of 39 QTLs were detected across eight different environments, of which five QTLs were stable. Forty-three candidate genes potentially involved in carbon metabolism, fatty acid synthesis and triacylglycerol biosynthesis processes were further obtained in the stable QTL regions. Transcriptome analysis showed that nineteen of these candidate genes expressed during the developing cottonseed ovules and may affect the cottonseed oil content. Besides, transcription factor (TF) and microRNA (miRNA) co-regulatory network analyses based on the nineteen candidate genes suggested that six genes, two core miRNAs (ghr-miR2949b and ghr-miR2949c), and one TF GhHSL1 were considered to be closely associated with the cottonseed oil content. Moreover, four vital genes were validated by quantitative real-time PCR (qRT-PCR). These results provide insights into the oil accumulation mechanism in developing cottonseed ovules through the construction of a detailed oil accumulation model.
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Jiang X, Gong J, Zhang J, Zhang Z, Shi Y, Li J, Liu A, Gong W, Ge Q, Deng X, Fan S, Chen H, Kuang Z, Pan J, Che J, Zhang S, Jia T, Wei R, Chen Q, Wei S, Shang H, Yuan Y. Quantitative Trait Loci and Transcriptome Analysis Reveal Genetic Basis of Fiber Quality Traits in CCRI70 RIL Population of Gossypium hirsutum. FRONTIERS IN PLANT SCIENCE 2021; 12:753755. [PMID: 34975939 PMCID: PMC8716697 DOI: 10.3389/fpls.2021.753755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 11/11/2021] [Indexed: 06/14/2023]
Abstract
Upland cotton (Gossypium hirsutum) is widely planted around the world for its natural fiber, and producing high-quality fiber is essential for the textile industry. CCRI70 is a hybrid cotton plant harboring superior yield and fiber quality, whose recombinant inbred line (RIL) population was developed from two upland cotton varieties (sGK156 and 901-001) and were used here to investigate the source of high-quality related alleles. Based on the material of the whole population, a high-density genetic map was constructed using specific locus-amplified fragment sequencing (SLAF-seq). It contained 24,425 single nucleotide polymorphism (SNP) markers, spanning a distance of 4,850.47 centimorgans (cM) over 26 chromosomes with an average marker interval of 0.20 cM. In evaluating three fiber quality traits in nine environments to detect multiple environments stable quantitative trait loci (QTLs), we found 289 QTLs, of which 36 of them were stable QTLs and 18 were novel. Based on the transcriptome analysis for two parents and two RILs, 24,941 unique differentially expressed genes (DEGs) were identified, 473 of which were promising genes. For the fiber strength (FS) QTLs, 320 DEGs were identified, suggesting that pectin synthesis, phenylpropanoid biosynthesis, and plant hormone signaling pathways could influence FS, and several transcription factors may regulate fiber development, such as GAE6, C4H, OMT1, AFR18, EIN3, bZIP44, and GAI. Notably, the marker D13_56413025 in qFS-chr18-4 provides a potential basis for enhancing fiber quality of upland cotton via marker-assisted breeding and gene cloning of important fiber quality traits.
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Yu X, Nai J, Guo H, Yang X, Deng X, Yuan X, Hua Y, Tian Y, Xu F, Zhang Z, Huang Y. Predicting the grades of Astragali radix using mass spectrometry-based metabolomics and machine learning. J Pharm Anal 2021; 11:611-616. [PMID: 34765274 PMCID: PMC8572717 DOI: 10.1016/j.jpha.2020.07.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 07/26/2020] [Accepted: 07/29/2020] [Indexed: 01/07/2023] Open
Abstract
Astragali radix (AR, the dried root of Astragalus) is a popular herbal remedy in both China and the United States. The commercially available AR is commonly classified into premium graded (PG) and ungraded (UG) ones only according to the appearance. To uncover novel sensitive and specific markers for AR grading, we took the integrated mass spectrometry-based untargeted and targeted metabolomics approaches to characterize chemical features of PG and UG samples in a discovery set (n=16 batches). A series of five differential compounds were screened out by univariate statistical analysis, including arginine, calycosin, ononin, formononetin, and astragaloside Ⅳ, most of which were observed to be accumulated in PG samples except for astragaloside Ⅳ. Then, we performed machine learning on the quantification data of five compounds and constructed a logistic regression prediction model. Finally, the external validation in an independent validation set of AR (n=20 batches) verified that the five compounds, as well as the model, had strong capability to distinguish the two grades of AR, with the prediction accuracy > 90%. Our findings present a panel of meaningful candidate markers that would significantly catalyze the innovation in AR grading.
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Razzaq A, Zafar MM, Li P, Qun G, Deng X, Ali A, Hafeez A, Irfan M, Liu A, Ren M, Shang H, Shi Y, Gong W, Yuan Y. Transformation and Overexpression of Primary Cell Wall Synthesis-Related Zinc Finger Gene Gh_A07G1537 to Improve Fiber Length in Cotton. FRONTIERS IN PLANT SCIENCE 2021; 12:777794. [PMID: 34804108 PMCID: PMC8604042 DOI: 10.3389/fpls.2021.777794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/18/2021] [Indexed: 06/01/2023]
Abstract
Molecular interventions have helped to explore the genes involved in fiber length, fiber strength, and other quality parameters with improved characteristics, particularly in cotton. The current study is an extension and functional validation of previous findings that Gh_A07G1537 influences fiber length in cotton using a chromosomal segment substitution line MBI7747 through RNA-seq data. The recombinant Gh_A07G1537 derived from the MBI7747 line was over-expressed in CCRI24, a genotype with a low profile of fiber quality parameters. Putative transformants were selected on MS medium containing hygromycin (25mg/ml), acclimatized, and shifted to a greenhouse for further growth and proliferation. Transgene integration was validated through PCR and Southern Blot analysis. Stable integration of the transgene (ΔGh_A07G1537) was validated by tracking its expression in different generations (T0, T1, and T2) of transformed cotton plants. It was found to be 2.97-, 2.86-, and 2.92-folds higher expression in T0, T1, and T2 plants, respectively, of transgenic compared with non-transgenic cotton plants. Fiber quality parameters were also observed to be improved in the engineered cotton line. Genetic modifications of Gh_A07G1537 support the improvement in fiber quality parameters and should be appreciated for the textile industry.
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Peng Y, Wu S, Liu Y, Chen M, Miao J, Zhao C, Chen S, Qi Z, Deng X. Synthetic CT Generation From Multi-Sequence MR Images for Head and Neck MRI-Only Radiotherapy via Cycle-Consistent Generative Adversarial Network. Int J Radiat Oncol Biol Phys 2021. [DOI: 10.1016/j.ijrobp.2021.07.1445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Xu S, Liu Y, Wen L, Zhao L, Deng X, Rong R, Lu J. [Application of Hydrashift 2/4 daratumumab assay in eliminating interference of daratumumab on serum immunofixation electrophoresis]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2021; 42:840-845. [PMID: 34788924 PMCID: PMC8607023 DOI: 10.3760/cma.j.issn.0253-2727.2021.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To investigate the interference of daratumumab on immunofixation electrophoresis after treating plasma cell diseases and methods to eliminate the interference. Methods: Serum samples of eight patients with plasma cell diseases treated with daratumumab in Peking University People's Hospital from April 2020 to March 2021 were collected for standard immunofixation electrophoresis and Hydrashift 2/4 daratumumab assay. Results: After treatment, 81.3% (13/16) of the samples showed drug-induced monoclonal antibodies (IgG-κ) . The samples without drug-induced monoclonal bands were related to individual differences, administration intervals, and immunoglobulin levels. Among the samples with IgG-κ monoclonal bands, 76.9% (10/13) could be directly identified as endogenous or exogenous monoclonal bands by immunofixation electrophoresis, and the others (3/13) could be identified by Hydrashift 2/4 daratumumab assay. Conclusion: Hydrashift 2/4 daratumumab assay can remove the band of daratumumab on the immunofixation electrophoresis and help with efficacy evaluation.
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Jin Y, Ye PP, Deng X, Wang Y, Er YL, Ji CR, Lu ZM, Duan LL. [Prevalence of injury among children in 28 counties of 6 provinces in China in 2017]. ZHONGHUA LIU XING BING XUE ZA ZHI = ZHONGHUA LIUXINGBINGXUE ZAZHI 2021; 42:1392-1400. [PMID: 34814559 DOI: 10.3760/cma.j.cn112338-20201112-01325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Objective: To investigate the incidence of injuries among children aged 0-17 years from 28 counties in six provinces. Methods: According to the earlier study on data in different local areas and the current work plan, we selected the survey objects for a general survey on child injury prevalence in the last 12 months. The subjects included guardians of children who did not attend kindergartens, children from kindergartens, and primary school grades 1-3. Children from grades 4-6 primary school, junior high school, and senior high school were also included. Results: The overall rate of injured children was 4.83%, with the incidence of injuries as 5.75% in the last 12 months before the survey. Both the rate of injured children and incidence of injuries were higher in boys than that in girls. Children whose primary caregivers were relatives, grandparents, minors, or with an education level below the primary school had a relatively higher rate of both injured children and incidence of injuries. The first cause of child injury was fall. The time of child injury was mainly from June to October, mainly at home, with the main activity as playing. The significant injuries in children were contusion and abrasion, and the main parts injured were lower limbs, upper limbs, and head. Most of the injuries were cured, and the primary treatment was outpatient and emergency treatment. Conclusions: Boys and children whose parents can not take care of are the priority population for child injury prevention and control. Targeted prevention and control measures should be implemented according to the characteristics of injuries among children of different ages.
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Lu ZM, Deng X, Wang Y, Er YL, Ye PP, Jin Y, Ji CR, Duan LL. [The epidemiological characteristics and influencing factors of animal injuries among children from 28 counties in 6 provinces, China]. ZHONGHUA LIU XING BING XUE ZA ZHI = ZHONGHUA LIUXINGBINGXUE ZAZHI 2021; 42:1401-1406. [PMID: 34814560 DOI: 10.3760/cma.j.cn112338-20201103-01299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Objective: To understand the epidemiological characteristic and influencing factors of animal injuries among children from 28 counties/districts in 6 provinces of China to provide evidence for formulating related prevention measures and strategies. Methods: Data was obtained from 'Children injury prevention project, 2016-2020'. Variables on the characteristics, including incidence, locations, related activities, time, and outcomes among children, were described. The negative binomial regression model analyzed animal injury frequency influencing factors. Results: There were 107 029 boys and 97 599 girls, with a gender ratio of 1.10, among the 204 628 children aged 0-17 in 28 counties/districts in 6 provinces of China. Per-person and per-time incidence rates of animal injuries were 0.70% and 0.72%, both higher in boys than in girls. Animal injuries among children mainly occurred in home (73.20%), road/street (7.51%), and open space of community/village (6.77%), during playing (63.15%), with the peak time between 12:01-18:00 (45.03%). Upper limbs (47.89%), lower limbs (35.31%), and head (8.44%) were the most injured body parts. Outpatient or emergency treatment (85.19%) had been carried out. The negative binomial regression showed that sex, grade, guardian educational level, urban or rural, and daily communication between guardians and children as influencing factors in the frequency of animal injuries among children. Conclusions: Special attention should be given to boys, at home, in projects on animal injury prevention and control. There were many influencing factors of animal injury frequency. Knowledge of injury prevention should be popularized to children and guardians. Related comprehensive intervention should be developed in families, schools, and social settings.
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Ji CR, Jin Y, Ye PP, Wang Y, Er YL, Deng X, Lu ZM, Duan LL. [Prevalence and prevention of traffic injury among children in 28 counties of 6 provinces in China, 2017]. ZHONGHUA LIU XING BING XUE ZA ZHI = ZHONGHUA LIUXINGBINGXUE ZAZHI 2021; 42:1407-1412. [PMID: 34814561 DOI: 10.3760/cma.j.cn112338-20201224-01440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Objective: To investigate the incidence of traffic injuries among children aged 0-17 years in 28 counties of 6 provinces and to provide prevention suggestions. Methods: Using the general survey method, a questionnaire survey was conducted on the road traffic injuries of children in 28 counties of 6 provinces in 2017. Results: A total of 204 628 students were surveyed, 908 of whom had experiences of road traffic injuries. Road traffic injuries were 0.44% among children in 28 counties of 6 provinces in China and 0.94% among children who did not attend kindergartens. July is a high incidence period of road traffic injuries among children (12.92%). When children suffer from road traffic injuries, the first three activities were playing (21.61%), riding an electric bicycle (20.40%), walking (20.07%). Most injuries appeared as contusion/abrasion, accounting for 42.26% of the total cases. The injured parts were mainly lower limbs, upper limbs, and heads, accounting for 38.85%, 23.29%, and 20.20%. Most children with road traffic injuries recovered after related treatments, accounting for 85.43% of all cases. The median length of hospital stay of children with road traffic injuries was seven days, and the median expense in hospitals was 3 000 Yuan (RMB). Conclusions: The incidence of road traffic injuries among males appeared higher than females, and the children who did not attend the kindergartens were the highest. During playing, riding an electric bicycle and walking were the top three activities prone to road traffic injuries.
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Wang SY, Pan XJ, Deng X, Zhang HJ, Chen ZP. [An exploratory framework of vaccine hesitancy monitoring and early warning system in China]. ZHONGHUA YU FANG YI XUE ZA ZHI [CHINESE JOURNAL OF PREVENTIVE MEDICINE] 2021; 55:925-930. [PMID: 34445829 DOI: 10.3760/cma.j.cn112150-20210501-00435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Vaccine hesitancy has spread worldwide recent years and resulting in increasing incidence of some well-controlled vaccine-preventable diseases, which is extremely unfavorable to the consolidation of the national immunization programme and the elimination of corresponding diseases. Based on the Complacency, Convenience and Confidence ("3Cs") model of vaccine hesitancy, combined with the practice experience of management of quality control through the whole vaccine life cycle in China, we introduce a framework of vaccine hesitancy monitoring and early warning in China to provide a reference for carrying out corresponding work. The indicator system of the framework derives from monitoring of vaccine life cycle quality management, population vaccine confidence, and service availability.
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Pang Y, Kosmin M, Li Z, Deng X, Li X, Zhang Y, Ding B, Royle G, Manolopoulos S. OC-0636 Utilising diffusion-weighted MRI for isotoxic dose escalated radiotherapy for glioblastoma. Radiother Oncol 2021. [DOI: 10.1016/s0167-8140(21)06992-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Kim W, Yoon D, Song Y, Koh Y, Cao J, Ji D, Yang H, Eom H, Jing H, Kwak J, Lee W, Lee J, Shin H, Jin J, Wang M, Li J, Huang X, Deng X, Yang Z, Zhu J. EARLY SAFETY AND EFFICACY DATA FROM A PHASE I/II TRIAL OF DZD4205, A SELECTIVE JAK1 INHIBITOR, IN RELAPSED/REFRACTORY PERIPHERAL T‐CELL LYMPHOMA. Hematol Oncol 2021. [DOI: 10.1002/hon.57_2879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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