112 results on '"Xiaokang Fu"'
Search Results
2. The value of dynamic changes in FT3 level for predicting 90-day prognosis of HBV-ACLF patients
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Jian Zhang, Luxue Zhang, Xiaokang Fu, Yu Chen, Zhongping Duan, and Geng Tian
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Acute-on-chronic liver failure ,FT3 ,Dynamic changes ,Prognosis ,Medicine - Abstract
Abstract Objective To explore the effect of dynamic changes in free triiodothyronine (FT3) level for predicting the 90 day prognosis of patients with hepatitis B virus–related acute-on-chronic liver failure (HBV-ACLF). Methods The clinical data of 122 hospitalised patients with HBV-ACLF between September 2018 and January 2020 were collected and divided into a survival group (77 cases) and a death group (45 cases) according to the 90 day prognosis. We statistically analysed the characteristics of FT3 changes in the two groups of patients. Binary logistic regression one-way analysis was used to assess the degree of influence of each factor. The Kaplan–Meier survival curve and receiver operating characteristic curve were used to evaluate the effect of a single change in FT3 level difference (single △FT3) and the FT3 level change range (△FT3 range) in predicting the 90-day prognosis of patients. Results There were only three types of changes in FT3 levels, which included 19 (15.6%) cases of continuous normal type, 35 (28.7%) cases of continuous decrease type and 68 (55.7%) cases of U-shaped change type. The difference in survival curves between the three types of patients was statistically significant (P
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- 2024
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3. Elevating the RRE Framework for Geospatial Analysis with Visual Programming Platforms: An Exploration with Geospatial Analytics Extension for KNIME
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Lingbo Liu, Fahui Wang, Xiaokang Fu, Tobias Kötter, Kevin Sturm, Weihe Wendy Guan, and Shuming Bao
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Geospatial Analysis ,Reproducibility, replicability, and expandability (RRE) ,Visual Programming ,Geospatial Analytics Extension for KNIME ,Geospatial Knowledge Tree ,Spatial Accessibility ,Physical geography ,GB3-5030 ,Environmental sciences ,GE1-350 - Abstract
Reproducibility, replicability, and expandability (RRE) have emerged as fundamental concerns in the realm of scientific research and development. Wherein, devising effective solutions for RRE within geospatial analysis stands out as a particularly critical challenge that demands immediate attention. Although there has been an evolution from basic reproducibility of code and data to a more comprehensive cyberinfrastructure, this integrated solution is still grappling with issues of limited user accessibility, steep learning curves particularly in coding skills, and difficulties in achieving collaboration with other data science platforms This study proposes a framework that combines open-source GIS with visual programming platforms, grounded in principles of standardization and educationalization, to advance the RRE framework in geographic analysis. Using the Geospatial Analytics Extension for KNIME as an example, we demonstrate the platform’s adaptability and utility through case studies in a recent textbook with an in-depth illustration of spatial accessibility analysis, specifically via the Generalized Two-Step Floating Catchment Area (G2SFCA) method. Our findings shed light on the transformative potential of such an integrative strategy, offer fresh perspectives for enhancing the RRE in geospatial analysis and craft a well-structured, intuitive, and extensive GIS knowledge tree.
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- 2024
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4. Mapping the landscape and roadmap of geospatial artificial intelligence (GeoAI) in quantitative human geography: An extensive systematic review
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Siqin Wang, Xiao Huang, Pengyuan Liu, Mengxi Zhang, Filip Biljecki, Tao Hu, Xiaokang Fu, Lingbo Liu, Xintao Liu, Ruomei Wang, Yuanyuan Huang, Jingjing Yan, Jinghan Jiang, Michaelmary Chukwu, Seyed Reza Naghedi, Moein Hemmati, Yaxiong Shao, Nan Jia, Zhiyang Xiao, Tian Tian, Yaxin Hu, Lixiaona Yu, Winston Yap, Edgardo Macatulad, Zhuo Chen, Yunhe Cui, Koichi Ito, Mengbi Ye, Zicheng Fan, Binyu Lei, and Shuming Bao
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Geospatial artificial intelligence ,GeoAI ,Human geography ,Geographic subdomains ,Systematic review ,Physical geography ,GB3-5030 ,Environmental sciences ,GE1-350 - Abstract
This paper brings a comprehensive systematic review of the application of geospatial artificial intelligence (GeoAI) in quantitative human geography studies, including the subdomains of cultural, economic, political, historical, urban, population, social, health, rural, regional, tourism, behavioural, environmental and transport geography. In this extensive review, we obtain 14,537 papers from the Web of Science in the relevant fields and select 1516 papers that we identify as human geography studies using GeoAI via human scanning conducted by several research groups around the world. We outline the GeoAI applications in human geography by systematically summarising the number of publications over the years, empirical studies across countries, the categories of data sources used in GeoAI applications, and their modelling tasks across different subdomains. We find out that existing human geography studies have limited capacity to monitor complex human behaviour and examine the non-linear relationship between human behaviour and its potential drivers—such limits can be overcome by GeoAI models with the capacity to handle complexity. We elaborate on the current progress and status of GeoAI applications within each subdomain of human geography, point out the issues and challenges, as well as propose the directions and research opportunities for using GeoAI in future human geography studies in the context of sustainable and open science, generative AI, and quantum revolution.
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- 2024
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5. Genome-wide analysis of SET domain genes and the function of GhSDG51 during salt stress in upland cotton (Gossypium hirsutum L.)
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Hongliang Jian, Fei Wei, Pengyun Chen, Tingli Hu, Xiaolan Lv, Bingqin Wang, Hantao Wang, Xiaohao Guo, Liang Ma, Jianhua Lu, Xiaokang Fu, Hengling Wei, and Shuxun Yu
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Gossypium ,SET domain-containing ,WGCNA ,Salt stress ,VIGS ,Botany ,QK1-989 - Abstract
Abstract Background Cotton, being extensively cultivated, holds immense economic significance as one of the most prominent crops globally. The SET (Su(var), E, and Trithorax) domain-containing protein is of significant importance in plant development, growth, and response to abiotic stress by modifying the lysine methylation status of histone. However, the comprehensive identification of SET domain genes (SDG) have not been conducted in upland cotton (Gossypium hirsutum L.). Results A total of 229 SDGs were identified in four Gossypium species, including G. arboretum, G. raimondii, G. hirsutum, and G. barbadense. These genes could distinctly be divided into eight groups. The analysis of gene structure and protein motif revealed a high degree of conservation among the SDGs within the same group. Collinearity analysis suggested that the SDGs of Gossypium species and most of the other selected plants were mainly expanded by dispersed duplication events and whole genome duplication (WGD) events. The allopolyploidization event also has a significant impact on the expansion of SDGs in tetraploid Gossypium species. Furthermore, the characteristics of these genes have been relatively conserved during the evolution. Cis-element analysis revealed that GhSDGs play a role in resistance to abiotic stresses and growth development. Furthermore, the qRT-PCR results have indicated the ability of GhSDGs to respond to salt stress. Co-expression analysis revealed that GhSDG51 might co-express with genes associated with salt stress. In addition, the silencing of GhSDG51 in cotton by the virus-induced gene silencing (VIGS) method suggested a potential positive regulatory role of GhSDG51 in salt stress. Conclusions The results of this study comprehensively analyze the SDGs in cotton and provide a basis for understanding the biological role of SDGs in the stress resistance in upland cotton.
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- 2023
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6. Comparison of endoscopic bilateral areolar and robotic-assisted bilateral axillo-breast approach thyroidectomy in differentiated thyroid carcinoma: a propensity-matched retrospective cohort study
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Xiaokang Fu, Yunhan Ma, Yiqi Hou, Yuan Liu, and Luming Zheng
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Differentiated thyroid carcinoma ,Bilateral axillo-breast approach robotic-assisted thyroidectomy ,Endoscopic bilateral areolar approach ,Propensity score-matched ,Surgery ,RD1-811 - Abstract
Abstract Background Robot-assisted and endoscopic thyroidectomy are superior to conventional open thyroidectomy in improving cosmetic outcomes and postoperative quality of life. The procedure of these thyroidectomies was similar in terms of surgical view, feasibility, and invasiveness. However, it remains uncertain whether the robotic-assisted bilateral axilla-breast approach (BABA) was superior to the endoscopic bilateral areolar approach (BAA) thyroidectomy. This study aimed to investigate the clinical benefit of these two surgical procedures to evaluate the difference between these two surgical procedures by comparing the pathological and surgical outcomes of endoscopic BAA and robotic-assisted BABA thyroidectomy in differentiated thyroid carcinoma. Methods From November 2018 to September 2021, 278 patients with differentiated thyroid carcinoma underwent BABA robot-assisted, and 49 underwent BAA approach endoscopic thyroidectomy. Of these patients, we analyzed 42 and 135 patients of endoscopic and robotic matched pairs using 1:4 propensity score matching and retrospective cohort study methods. These two groups were retrospectively compared by surgical outcomes, clinicopathological characteristics, and postoperative complications. Results The mean operation time was significantly longer in the EG than in the RG (p
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- 2023
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7. Geospatial Analytics Extension for KNIME
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Lingbo Liu, Xiaokang Fu, Tobias Kötter, Kevin Sturm, Carsten Haubold, Weihe Wendy Guan, Shuming Bao, and Fahui Wang
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Geospatial analytics ,KNIME analytics platform ,GIS ,Visual programming ,Replicability and reproducibility ,Computer software ,QA76.75-76.765 - Abstract
The Geospatial Analytics Extension for KNIME (GAEK) is an innovative tool designed to integrate visual programming with geospatial analytics, streamlining GIS education and research in social sciences. GAEK simplifies access for users with an intuitive, visual interface for complex spatial analysis tasks and contributes to the organization of the GIS Knowledge Tree through its geospatial analytics nodes. This paper discusses GAEK's architecture, functionalities, and its transformative impact on GIS applications. While GAEK significantly enhances user experience and research reproducibility, future updates aim to expand its functionality and optimize its bundled environment.
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- 2024
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8. A systematic analysis of the phloem protein 2 (PP2) proteins in Gossypium hirsutum reveals that GhPP2-33 regulates salt tolerance
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Fei Wei, Pengyun Chen, Hongliang Jian, Xiaohao Guo, Xiaoyan Lv, Boying Lian, Mengxi Sun, Li An, Xinyu Dang, Miaoqian Yang, Hongmei Wu, Nan Zhang, Aimin Wu, Hantao Wang, Liang Ma, Xiaokang Fu, Jianhua Lu, Shuxun Yu, and Hengling Wei
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Gossypium hirsutum ,Phloem protein 2 ,Salt stress ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Phloem protein 2 (PP2) proteins play a vital role in the Phloem-based defense (PBD) and participate in many abiotic and biotic stress. However, research on PP2 proteins in cotton is still lacking. Results A total of 25, 23, 43, and 47 PP2 genes were comprehensively identified and characterized in G.arboretum, G.raimondii, G.barbadense, and G.hirsutum. The whole genome duplication (WGD) and allopolyploidization events play essential roles in the expansion of PP2 genes. The promoter regions of GhPP2 genes contain many cis-acting elements related to abiotic stress and the weighted gene co-expression network analysis (WGCNA) analysis displayed that GhPP2s could be related to salt stress. The qRT-PCR assays further confirmed that GhPP2-33 could be dramatically upregulated during the salt treatment. And the virus-induced gene silencing (VIGS) experiment proved that the silencing of GhPP2-33 could decrease salt tolerance. Conclusions The results in this study not only offer new perspectives for understanding the evolution of PP2 genes in cotton but also further explore their function under salt stress.
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- 2023
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9. Effects of Different Treatments on the Structure and Physicochemical Properties of Artichoke Dietary Fiber
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Yayi WANG, Xiaokang FU, Bian HE, Liang HUANG, Renwei ZHU, and Linwei ZHANG
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artichokes ,dietary fiber ,freezing ,ultrafine grinding ,physicochemical properties ,Food processing and manufacture ,TP368-456 - Abstract
The effects of two treatments–ultrafine grinding (UG) and freeze-ultrafine-grinding (FUG) on the structure and physicochemical properties of artichoke dietary fiber as dietary fiber (ADF) were investigated. The results showed that the structure of the freeze-ultrafine-grinding artichoke dietary fiber was looser and the particle size was more uniform and concentrated. Compared with non-treated ADF, the D50 values were reduced by 84.63% and 86.72% respectively for the two treatments. In addition, the swelling power, the water holding capacity and the oil holding capacity of the two treatments were increased by 1.22, 1.20, 1.06 times and 1.44, 1.25, 1.97 times, respectively. Moreover, the glucose absorption capacity were increased by 135.09% and 271.09%. And beyond that, the crystallinity of non-treated ADF, UG and FUG were 26.73%, 30.57% and 38.10%. Both UG and FUG improved the physicochemical properties of artichoke dietary fiber, with the latter one being more effective. This study would provide new ideas for the comprehensive utilization of artichoke dietary fiber in the future.
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- 2022
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10. Systematic analysis of CNGCs in cotton and the positive role of GhCNGC32 and GhCNGC35 in salt tolerance
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Zhengying Lu, Guo Yin, Mao Chai, Lu Sun, Hengling Wei, Jie Chen, Yufeng Yang, Xiaokang Fu, and Shiyun Li
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Cotton ,GhCNGC genes ,Salt tolerance ,Abscisic acid ,Abiotic stress ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Cyclic nucleotide-gated ion channels (CNGCs) are calcium-permeable channels that participate in a variety of biological functions, such as signaling pathways, plant development, and environmental stress and stimulus responses. Nevertheless, there have been few studies on CNGC gene family in cotton. Results In this study, a total of 114 CNGC genes were identified from the genomes of 4 cotton species. These genes clustered into 5 main groups: I, II, III, IVa, and IVb. Gene structure and protein motif analysis showed that CNGCs on the same branch were highly conserved. In addition, collinearity analysis showed that the CNGC gene family had expanded mainly by whole-genome duplication (WGD). Promoter analysis of the GhCNGCs showed that there were a large number of cis-acting elements related to abscisic acid (ABA). Combination of transcriptome data and the results of quantitative RT–PCR (qRT–PCR) analysis revealed that some GhCNGC genes were induced in response to salt and drought stress and to exogenous ABA. Virus-induced gene silencing (VIGS) experiments showed that the silencing of the GhCNGC32 and GhCNGC35 genes decreased the salt tolerance of cotton plants (TRV:00). Specifically, physiological indexes showed that the malondialdehyde (MDA) content in gene-silenced plants (TRV:GhCNGC32 and TRV:GhCNGC35) increased significantly under salt stress but that the peroxidase (POD) activity decreased. After salt stress, the expression level of ABA-related genes increased significantly, indicating that salt stress can trigger the ABA signal regulatory mechanism. Conclusions we comprehensively analyzed CNGC genes in four cotton species, and found that GhCNGC32 and GhCNGC35 genes play an important role in cotton salt tolerance. These results laid a foundation for the subsequent study of the involvement of cotton CNGC genes in salt tolerance.
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- 2022
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11. Public Surveillance of Social Media for Suicide Using Advanced Deep Learning Models in Japan: Time Series Study From 2012 to 2022
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Siqin Wang, Huan Ning, Xiao Huang, Yunyu Xiao, Mengxi Zhang, Ellie Fan Yang, Yukio Sadahiro, Yan Liu, Zhenlong Li, Tao Hu, Xiaokang Fu, Zi Li, and Ye Zeng
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Computer applications to medicine. Medical informatics ,R858-859.7 ,Public aspects of medicine ,RA1-1270 - Abstract
BackgroundSocial media platforms have been increasingly used to express suicidal thoughts, feelings, and acts, raising public concerns over time. A large body of literature has explored the suicide risks identified by people’s expressions on social media. However, there is not enough evidence to conclude that social media provides public surveillance for suicide without aligning suicide risks detected on social media with actual suicidal behaviors. Corroborating this alignment is a crucial foundation for suicide prevention and intervention through social media and for estimating and predicting suicide in countries with no reliable suicide statistics. ObjectiveThis study aimed to corroborate whether the suicide risks identified on social media align with actual suicidal behaviors. This aim was achieved by tracking suicide risks detected by 62 million tweets posted in Japan over a 10-year period and assessing the locational and temporal alignment of such suicide risks with actual suicide behaviors recorded in national suicide statistics. MethodsThis study used a human-in-the-loop approach to identify suicide-risk tweets posted in Japan from January 2013 to December 2022. This approach involved keyword-filtered data mining, data scanning by human efforts, and data refinement via an advanced natural language processing model termed Bidirectional Encoder Representations from Transformers. The tweet-identified suicide risks were then compared with actual suicide records in both temporal and spatial dimensions to validate if they were statistically correlated. ResultsTwitter-identified suicide risks and actual suicide records were temporally correlated by month in the 10 years from 2013 to 2022 (correlation coefficient=0.533; P
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- 2023
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12. GhDof1.7, a Dof Transcription Factor, Plays Positive Regulatory Role under Salinity Stress in Upland Cotton
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Yi Li, Miaomiao Tian, Zhen Feng, Jingjing Zhang, Jianhua Lu, Xiaokang Fu, Liang Ma, Hengling Wei, and Hantao Wang
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upland cotton ,DNA-binding with one finger ,ABA ,H2O2 ,salt stress ,Botany ,QK1-989 - Abstract
Salt stress is a major abiotic stressor that can severely limit plant growth, distribution, and crop yield. DNA-binding with one finger (Dof) is a plant-specific transcription factor that plays a crucial role in plant growth, development, and stress response. In this study, the function of a Dof transcription factor, GhDof1.7, was investigated in upland cotton. The GhDof1.7 gene has a coding sequence length of 759 base pairs, encoding 252 amino acids, and is mainly expressed in roots, stems, leaves, and inflorescences. Salt and abscisic acid (ABA) treatments significantly induced the expression of GhDof1.7. The presence of GhDof1.7 in Arabidopsis may have resulted in potential improvements in salt tolerance, as suggested by a decrease in H2O2 content and an increase in catalase (CAT) and superoxide dismutase (SOD) activities. The GhDof1.7 protein was found to interact with GhCAR4 (C2-domain ABA-related 4), and the silencing of either GhDof1.7 or GhCAR4 resulted in reduced salt tolerance in cotton plants. These findings demonstrate that GhDof1.7 plays a crucial role in improving the salt tolerance of upland cotton and provide insight into the regulation of abiotic stress response by Dof transcription factors.
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- 2023
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13. Ceiling temperature distribution and decay in tunnel fires: Effect of longitudinal velocity, bifurcated shaft exhaust and fire location
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Liangliang Tao, Yanhua Zeng, Guichang Yang, Dongxu Zhao, Jie Li, and Xiaokang Fu
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Tunnel fire ,Fire location ,Bifurcated shaft ,Longitudinal velocity ,Temperature distribution ,Temperature decay ,Engineering (General). Civil engineering (General) ,TA1-2040 - Abstract
This paper establishes a model tunnel to investigate the impact of longitudinal velocity (u), bifurcated shaft exhaust velocity (BSEV) and fire location on ceiling temperature and decay. The experimental results show that a longitudinal velocity of 0.6 m/s can control the upstream high temperature within 2.5 m when the distance between fire and shaft (D) is 1.0 m, and further increase in longitudinal velocity has little effect on upstream temperature distribution. Downstream temperature profile should be divided into two cases according to the magnitude of longitudinal velocity: the difference between the temperature decay model in low-speed region (u ≤ 0.5 m/s) and that in the high-speed region (u > 0.5 m/s) is particularly obvious with D at 1.0 m, and the downstream temperature decay rate in the low-speed region is the slowest compared to all the working conditions in this paper. For D more than 1.0 m, the range of high temperature distribution increases with D for certain longitudinal velocities (0.6-0.7 m/s); however, at particularly large longitudinal velocity (0.8 m/s), D has almost no effect on the upstream temperature distribution. The effect of longitudinal velocity on upstream temperature is stronger than that of BSEV. The downstream ceiling temperature decay model is little affected by longitudinal velocity and BSEV with D more than 1.0 m. The temperature decay rate first decreases, then increases, and finally decreases again as the D increases. Existing temperature attenuation models cannot predict the temperature profile in longitudinally ventilated tunnels with BSEV, but the temperature decay model considering fire location proposed in this paper can provide a reference value for tunnels with synergistic ventilation of longitudinal ventilation and BSEV.
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- 2023
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14. Human mobility and COVID-19 transmission: a systematic review and future directions
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Mengxi Zhang, Siqin Wang, Tao Hu, Xiaokang Fu, Xiaoyue Wang, Yaxin Hu, Briana Halloran, Zhenlong Li, Yunhe Cui, Haokun Liu, Zhimin Liu, and Shuming Bao
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Human mobility ,COVID-19 transmission ,systematic review ,mobility data ,mathematical modelling ,Mathematical geography. Cartography ,GA1-1776 - Abstract
Without a widely distributed vaccine, controlling human mobility has been identified and promoted as the primary strategy to mitigate the transmission of COVID-19. Many studies have reported the relationship between human mobility and COVID-19 transmission by utilizing the spatial-temporal information of mobility data from various sources. To better understand the role of human mobility in the pandemic, we conducted a systematic review of articles that measure the relationship between human mobility and COVID-19 in terms of their data sources, mathematical models, and key findings. Following the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement, we selected 47 articles from the Web of Science Core Collection up to September 2020. Restricting human mobility reduced the transmission of COVID-19, although the effectiveness and stringency of policy implementation vary temporally and spatially across different stages of the pandemic. We call for prompt and sustainable measures to control the pandemic. We also recommend researchers 1) to enhance multi-disciplinary collaboration; 2) to adjust the implementation and stringency of mobility-control policies in corresponding to the rapid change of the pandemic; 3) to improve mathematical models used in analysing, simulating, and predicting the transmission of the disease; and 4) to enrich the source of mobility data to ensure data accuracy and suability.
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- 2022
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15. An evaluation method for types of low-production coalbed methane reservoirs and its application
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Xiaoming Ni, Xuebin Tan, Baoyu Wang, and Xiaokang Fu
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Type of low-production CBM reservoir ,Desorption ,Diffusion and seepage ,Analytical hierarchy process ,Logging curve ,Electrical engineering. Electronics. Nuclear engineering ,TK1-9971 - Abstract
At present, the macro-parameters such as critical desorption pressure, comprehensive diffusion coefficient, and permeability are commonly used to characterize the properties of a reservoir, and the productivity of coalbed methane (CBM) wells can be predicted through numerical simulation or established mathematical models, and the types of low-producing CBM reservoirs can be classified. However, low production from CBM wells is often caused by the weakness of one (or more) of desorption, diffusion, and seepage in CBM reservoirs, and the evaluation of a single link and macro-parametric characterization of reservoir properties cannot really ascertain the cause of the low production from a given CBM well.In the present work, the influences of pores and fracture structure, fluid flow dynamics and resistance on the desorption, diffusion, and seepage of CBM were considered from the perspective of system theory, and the evaluative parameter index system of low-productivity reservoirs was established. This avoids the one-sidedness of the evaluative results arising when only considering macro-parameters. New methods of obtaining the evaluative parameters pertaining to desorption, diffusion, and seepage are proposed: the methods include isothermal adsorption experiments, the use of logging curves, drainage data, mercury injection, and a classical mathematical model. These methods combined the data from experiments with in-situ data, and ensure the accuracy and practicability of the resulting evaluative parameters. On this basis, types of low-production reservoirs were classified using an analytic hierarchy process with multi-parameter superposition.The evaluative results pertaining to Shizhuang North block in the Qinshui Basin, Shanxi Province, China show that there are six types of low-yield reservoirs among the evaluative wells tested. Among them, diffusion is the main factor governing the low yield of CBM wells, followed by desorption and seepage. Herein, the reservoir constraint on CBM production is comprehensively evaluated, identifying the main controlling link affecting the low productivity of CBM wells, and laying a theoretical foundation for targeted transformation measures.
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- 2021
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16. Human mobility data in the COVID-19 pandemic: characteristics, applications, and challenges
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Tao Hu, Siqin Wang, Bing She, Mengxi Zhang, Xiao Huang, Yunhe Cui, Jacob Khuri, Yaxin Hu, Xiaokang Fu, Xiaoyue Wang, Peixiao Wang, Xinyan Zhu, Shuming Bao, Wendy Guan, and Zhenlong Li
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covid-19 ,public health ,human mobility ,open data ,mobile phone ,mobility index ,Mathematical geography. Cartography ,GA1-1776 - Abstract
The COVID-19 pandemic poses unprecedented challenges around the world. Many studies have applied mobility data to explore spatiotemporal trends over time, investigate associations with other variables, and predict or simulate the spread of COVID-19. Our objective was to provide a comprehensive overview of human mobility open data to guide researchers and policymakers in conducting data-driven evaluations and decision-making for the COVID-19 pandemic and other infectious disease outbreaks. We summarized the mobility data usage in COVID-19 studies by reviewing recent publications on COVID-19 and human mobility from a data-oriented perspective. We identified three major sources of mobility data: public transit systems, mobile operators, and mobile phone applications. Four approaches have been commonly used to estimate human mobility: public transit-based flow, social activity patterns, index-based mobility data, and social media-derived mobility data. We compared mobility datasets’ characteristics by assessing data privacy, quality, space–time coverage, high-performance data storage and processing, and accessibility. We also present challenges and future directions of using mobility data. This review makes a pivotal contribution to understanding the use of and access to human mobility data in the COVID-19 pandemic and future disease outbreaks.
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- 2021
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17. PKIB involved in the metastasis and survival of osteosarcoma
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Rongxue Wan, Gu Yang, Qianzhen Liu, Xiaokang Fu, Zengping Liu, Huilai Miao, Huan Liu, and Wenhua Huang
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PKIB ,metastasis ,AIM2 ,osteosarcoma ,Akt ,nomogram ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Osteosarcoma is frequently metastasized at the time of diagnosis in patients. However, the underlying mechanism of osteosarcoma metastasis remains poorly understood. In this study, we evaluated DNA methylation profiles combined with gene expression profiles of 21 patients with metastatic osteosarcoma and 64 patients with non-metastatic osteosarcoma from TARGET database and identified PKIB and AIM2 as hub genes related to the metastasis of osteosarcoma. To verify the effects of PKIB on migration and invasion of osteosarcoma, we performed wound-healing assay and transwell assay. The results showed that PKIB significantly inhibited the migration and invasion of osteosarcoma cells, and the Western blot experiments showed that the protein level of E-cad was upregulated and of VIM was downregulated in 143-B cell recombinant expression PKIB. These results indicate that PKIB inhibit the metastasis of osteosarcoma. CCK-8 assay results showed that PKIB promote the proliferation of osteosarcoma. In addition, the Western blot results showed that the phosphorylation level of Akt was upregulated in 143-B cells overexpressing PKIB, indicating that PKIB promotes the proliferation of osteosarcoma probably through signaling pathway that Akt involved in. These results give us clues that PKIB was a potential target for osteosarcoma therapy. Furthermore, combined clinical profiles analysis showed that the expression of AIM2- and PKIB- related risk scores was significantly related to the overall survival of patients with osteosarcoma. Thus, we constructed a nomogram based on AIM2 and PKIB expression–related risk scores for osteosarcoma prognostic assessment to predict the 1-, 2-, 3-, and 5-year overall survival rate of patients with metastatic osteosarcoma, assisting clinicians in the diagnosis and treatment of metastatic osteosarcoma.
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- 2022
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18. Comprehensive identification and expression analysis of B-Box genes in cotton
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Zhen Feng, Mengyu Li, Yi Li, Xu Yang, Hengling Wei, Xiaokang Fu, Liang Ma, Jianhua Lu, Hantao Wang, and Shuxun Yu
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G. hirsutum ,BBX ,flower bud differentiation ,phytohormone ,stress response ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background B-BOX (BBX) proteins are zinc-finger transcription factors with one or two BBX domains and sometimes a CCT domain. These proteins play an essential role in regulating plant growth and development, as well as in resisting abiotic stress. So far, the BBX gene family has been widely studied in other crops. However, no one has systematically studied the BBX gene in cotton. Results In the present study, 17, 18, 37 and 33 BBX genes were detected in Gossypium arboreum, G. raimondii, G. hirsutum and G. barbadense, respectively, via genome-wide identification. Phylogenetic analysis showed that all BBX genes were divided into 5 main categories. The protein motifs and exon/intron structures showed that each group of BBX genes was highly conserved. Collinearity analysis revealed that the amplification of BBX gene family in Gossypium spp. was mainly through segmental replication. Nonsynonymous (Ka)/ synonymous (Ks) substitution ratios indicated that the BBX gene family had undergone purification selection throughout the long-term natural selection process. Moreover, transcriptomic data showed that some GhBBX genes were highly expressed in floral organs. The qRT-PCR results showed that there were significant differences in GhBBX genes in leaves and shoot apexes between early-maturing materials and late-maturing materials at most periods. Yeast two-hybrid results showed that GhBBX5/GhBBX23 and GhBBX8/GhBBX26 might interact with GhFT. Transcriptome data analysis and qRT-PCR verification showed that different GhBBX genes had different biological functions in abiotic stress and phytohormone response. Conclusions Our comprehensive analysis of BBX in G. hirsutum provided a basis for further study on the molecular role of GhBBXs in regulating flowering and cotton resistance to abiotic stress.
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- 2021
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19. The CCCH-Type Zinc-Finger Protein GhC3H20 Enhances Salt Stress Tolerance in Arabidopsis thaliana and Cotton through ABA Signal Transduction Pathway
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Qi Zhang, Jingjing Zhang, Fei Wei, Xiaokang Fu, Hengling Wei, Jianhua Lu, Liang Ma, and Hantao Wang
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cotton ,GhC3H20 ,salt stress ,GhPP2CA and GhHAB1 ,ABA signaling pathway ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
The CCCH zinc-finger protein contains a typical C3H-type motif widely existing in plants, and it plays an important role in plant growth, development, and stress responses. In this study, a CCCH zinc-finger gene, GhC3H20, was isolated and thoroughly characterized to regulate salt stress in cotton and Arabidopsis. The expression of GhC3H20 was up-regulated under salt, drought, and ABA treatments. GUS activity was detected in the root, stem, leaves, and flowers of ProGhC3H20::GUS transgenic Arabidopsis. Compared with the control, the GUS activity of ProGhC3H20::GUS transgenic Arabidopsis seedlings under NaCl treatment was stronger. Through the genetic transformation of Arabidopsis, three transgenic lines of 35S-GhC3H20 were obtained. Under NaCl and mannitol treatments, the roots of the transgenic lines were significantly longer than those of the wild-type (WT) Arabidopsis. The leaves of the WT turned yellow and wilted under high-concentration salt treatment at the seedling stage, while the leaves of the transgenic Arabidopsis lines did not. Further investigation showed that compared with the WT, the content of catalase (CAT) in the leaves of the transgenic lines was significantly higher. Therefore, compared with the WT, overexpression of GhC3H20 enhanced the salt stress tolerance of transgenic Arabidopsis. A virus-induced gene silencing (VIGS) experiment showed that compared with the control, the leaves of pYL156-GhC3H20 plants were wilted and dehydrated. The content of chlorophyll in pYL156-GhC3H20 leaves was significantly lower than those of the control. Therefore, silencing of GhC3H20 reduced salt stress tolerance in cotton. Two interacting proteins (GhPP2CA and GhHAB1) of GhC3H20 have been identified through a yeast two-hybrid assay. The expression levels of PP2CA and HAB1 in transgenic Arabidopsis were higher than those in the WT, and pYL156-GhC3H20 had expression levels lower than those in the control. GhPP2CA and GhHAB1 are the key genes involved in the ABA signaling pathway. Taken together, our findings demonstrate that GhC3H20 may interact with GhPP2CA and GhHAB1 to participate in the ABA signaling pathway to enhance salt stress tolerance in cotton.
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- 2023
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20. Evolution and Stress Responses of CLO Genes and Potential Function of the GhCLO06 Gene in Salt Resistance of Cotton
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Xiaokang Fu, Yonglin Yang, Meng Kang, Hengling Wei, Boying Lian, Baoquan Wang, Liang Ma, Pengbo Hao, Jianhua Lu, Shuxun Yu, and Hantao Wang
- Subjects
cotton ,caleosin protein ,salt tolerance ,abscisic acid ,GhCLO06 ,Plant culture ,SB1-1110 - Abstract
The caleosin (CLO) protein family displays calcium-binding properties and plays an important role in the abiotic stress response. Here, a total of 107 CLO genes were identified in 15 plant species, while no CLO genes were detected in two green algal species. Evolutionary analysis revealed that the CLO gene family may have evolved mainly in terrestrial plants and that biological functional differentiation between species and functional expansion within species have occurred. Of these, 56 CLO genes were identified in four cotton species. Collinearity analysis showed that CLO gene family expansion mainly occurred through segmental duplication and whole-genome duplication in cotton. Sequence alignment and phylogenetic analysis showed that the CLO proteins of the four cotton species were mainly divided into two types: H-caleosins (class I) and L-caleosins (class II). Cis-acting element analysis and quantitative RT–PCR (qRT–PCR) suggested that GhCLOs might be regulated by abscisic acid (ABA) and methyl jasmonate (MeJA). Moreover, transcriptome data and qRT–PCR results revealed that GhCLO genes responded to salt and drought stresses. Under salt stress, gene-silenced plants (TRV: GhCLO06) showed obvious yellowing and wilting, higher malondialdehyde (MDA) content accumulation, and significantly lower activities of superoxide dismutase (SOD) and peroxidase (POD), indicating that GhCLO06 plays a positive regulatory role in cotton salt tolerance. In gene-silenced plants (TRV: GhCLO06), ABA-related genes (GhABF2, GhABI5, and GhNAC4) were significantly upregulated after salt stress, suggesting that the regulation of salt tolerance may be related to the ABA signaling pathway. This research provides an important reference for further understanding and analyzing the molecular regulatory mechanism of CLOs for salt tolerance.
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- 2022
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21. Genome-wide identification and expression patterns analysis of the RPD3/HDA1 gene family in cotton
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Jingjing Zhang, Aimin Wu, Hengling Wei, Pengbo Hao, Qi Zhang, Miaomiao Tian, Xu Yang, Shuaishuai Cheng, Xiaokang Fu, Liang Ma, Hantao Wang, and Shuxun Yu
- Subjects
Gossypium ,Histone deacetylases ,Expression patterns ,Abiotic stress ,Early maturity ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Histone deacetylases (HDACs) catalyze histone deacetylation and suppress gene transcription during various cellular processes. Within the superfamily of HDACs, RPD3/HDA1-type HDACs are the most studied, and it is reported that RPD3 genes play crucial roles in plant growth and physiological processes. However, there is a lack of systematic research on the RPD3/HDA1 gene family in cotton. Results In this study, genome-wide analysis identified 9, 9, 18, and 18 RPD3 genes in Gossypium raimondii, G. arboreum, G. hirsutum, and G. barbadense, respectively. This gene family was divided into 4 subfamilies through phylogenetic analysis. The exon-intron structure and conserved motif analysis revealed high conservation in each branch of the cotton RPD3 genes. Collinearity analysis indicated that segmental duplication was the primary driving force during the expansion of the RPD3 gene family in cotton. There was at least one presumed cis-element related to plant hormones in the promoter regions of all GhRPD3 genes, especially MeJA- and ABA-responsive elements, which have more members than other hormone-relevant elements. The expression patterns showed that most GhRPD3 genes had relatively high expression levels in floral organs and performed higher expression in early-maturity cotton compared with late-maturity cotton during flower bud differentiation. In addition, the expression of GhRPD3 genes could be significantly induced by one or more abiotic stresses as well as exogenous application of MeJA or ABA. Conclusions Our findings reveal that GhRPD3 genes may be involved in flower bud differentiation and resistance to abiotic stresses, which provides a basis for further functional verification of GhRPD3 genes in cotton development and a foundation for breeding better early-maturity cotton cultivars in the future.
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- 2020
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22. Community Evolutional Network for Situation Awareness Using Social Media
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Xiaokang Fu, Yandong Wang, Mengmeng Li, Mingxuan Dou, Mengling Qiao, and Kai Hu
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Co-word network ,community evolution ,topic evolution ,situational awareness ,Electrical engineering. Electronics. Nuclear engineering ,TK1-9971 - Abstract
Social media is important for situational awareness during a disaster. During a disaster, the situation of emergence often changes over time and hence the topics of social media messages generated by social media users also change accordingly. Few studies quantitatively describe the topic evolution of social media during a disaster and the corresponding relationship between topic evolution and disaster process. We address this problem using co-word network analysis and present a new method based on the community evolution of the co-word network to analyze topic evolution over time in social media. The method uses communities of the co-word network in social media to represent topics. Based on the theory of community evolution, a community evolutional network is proposed to support and quantify the evolution of the topics. We implemented the proposed method in a case study, “July 2012 Beijing flood” using the Sina Weibo dataset. Results show that our method can well quantify the evolution process of topics and validate the effectiveness of our method in real-world applications. The method can facilitate the understanding of public expression dynamics during a disaster and be used to reveal the process and stages of a disaster.
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- 2020
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23. A Comprehensive Analysis of the DUF4228 Gene Family in Gossypium Reveals the Role of GhDUF4228-67 in Salt Tolerance
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Xiaoyan Lv, Fei Wei, Boying Lian, Guo Yin, Mengxi Sun, Pengyun Chen, Li An, Hongliang Jian, Hantao Wang, Xiaokang Fu, Liang Ma, Jianhua Lu, Baoquan Wang, and Hengling Wei
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Gossypium ,domains of unknown function 4228 (DUF4228) ,VIGS ,salt stress ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Soil salinization conditions seriously restrict cotton yield and quality. Related studies have shown that the DUF4228 proteins are pivotal in plant resistance to abiotic stress. However, there has been no systematic identification and analysis of the DUF4228 gene family in cotton and their role in abiotic stress. In this study, a total of 308 DUF4228 genes were identified in four Gossypium species, which were divided into five subfamilies. Gene structure and protein motifs analysis showed that the GhDUF4228 proteins were conserved in each subfamily. In addition, whole genome duplication (WGD) events and allopolyploidization might play an essential role in the expansion of the DUF4228 genes. Besides, many stress-responsive (MYB, MYC) and hormone-responsive (ABA, MeJA) related cis-elements were detected in the promoters of the DUF4228 genes. The qRT-PCR results showed that GhDUF4228 genes might be involved in the response to abiotic stress. VIGS assays and the measurement of relative water content (RWC), Proline content, POD activity, and malondialdehyde (MDA) content indicated that GhDUF4228-67 might be a positive regulator of cotton response to salt stress. The results in this study systematically characterized the DUF4228s in Gossypium species and will provide helpful information to further research the role of DUF4228s in salt tolerance.
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- 2022
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24. A Comprehensive Gene Co-Expression Network Analysis Reveals a Role of GhWRKY46 in Responding to Drought and Salt Stresses
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Pengyun Chen, Fei Wei, Hongliang Jian, Tingli Hu, Baoquan Wang, Xiaoyan Lv, Hantao Wang, Xiaokang Fu, Shuxun Yu, Hengling Wei, and Liang Ma
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cotton ,transcriptomic ,abiotic stresses ,WGCNA ,VIGS ,GhWRKY46 ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Abiotic stress, such as drought and salinity stress, seriously inhibit the growth and development of plants. Therefore, it is vital to understand the drought and salinity resistance mechanisms to enable cotton to provide more production under drought and salt conditions. In this study, we identified 8806 and 9108 differentially expressed genes (DEGs) through a comprehensive analysis of transcriptomic data related to the PEG-induced osmotic and salt stress in cotton. By performing weighted gene co-expression network analysis (WGCNA), we identified four co-expression modules in PEG treatment and five co-expression modules in salinity stress, which included 346 and 324 predicted transcription factors (TFs) in these modules, respectively. Correspondingly, whole genome duplication (WGD) events mainly contribute to the expansion of those TFs. Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) analyses revealed those different modules were associated with stress resistance, including regulating macromolecule metabolic process, peptidase activity, transporter activity, lipid metabolic process, and responses to stimulus. Quantitative RT-PCR analysis was used to confirm the expression levels of 15 hub TFs in PEG6000 and salinity treatments. We found that the hub gene GhWRKY46 could alter salt and PEG-induced drought resistance in cotton through the virus-induced gene silencing (VIGS) method. Our results provide a preliminary framework for further investigation of the cotton response to salt and drought stress, which is significant to breeding salt- and drought-tolerant cotton varieties.
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- 2022
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25. Genome-Wide Identification of the Early Flowering 4 (ELF4) Gene Family in Cotton and Silent GhELF4-1 and GhEFL3-6 Decreased Cotton Stress Resistance
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Miaomiao Tian, Aimin Wu, Meng Zhang, Jingjing Zhang, Hengling Wei, Xu Yang, Liang Ma, Jianhua Lu, Xiaokang Fu, Hantao Wang, and Shuxun Yu
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ELF4 ,cotton ,fiber ,expression patterns ,gene silencing ,Genetics ,QH426-470 - Abstract
The early flowering 4 (ELF4) family members play multiple roles in the physiological development of plants. ELF4s participated in the plant biological clock’s regulation process, photoperiod, hypocotyl elongation, and flowering time. However, the function in the ELF4s gene is barely known. In this study, 11, 12, 21, and 22 ELF4 genes were identified from the genomes of Gossypium arboreum, Gossypium raimondii, Gossypium hirsutum, and Gossypium barbadense, respectively. There ELF4s genes were classified into four subfamilies, and members from the same subfamily show relatively conservative gene structures. The results of gene chromosome location and gene duplication revealed that segmental duplication promotes gene expansion, and the Ka/Ks indicated that the ELF4 gene family has undergone purification selection during long-term evolution. Spatio-temporal expression patterns and qRT-PCR showed that GhELF4 genes were mainly related to flower, leaf, and fiber development. Cis-acting elements analysis and qRT-PCR showed that GhELF4 genes might be involved in the regulation of abscisic acid (ABA) or light pathways. Silencing of GhELF4-1 and GhEFL3-6 significantly affected the height of cotton seedlings and reduced the resistance of cotton. The identification and functional analysis of ELF4 genes in upland cotton provide more candidate genes for genetic modification.
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- 2021
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26. Corrigendum: Genome-Wide Identification and Expression Pattern Analysis of the HAK/KUP/KT Gene Family of Cotton in Fiber Development and Under Stresses
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Xu Yang, Jingjing Zhang, Aimin Wu, Hengling Wei, Xiaokang Fu, Miaomiao Tian, Liang Ma, Jianhua Lu, Hantao Wang, and Shuxun Yu
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HAK/KUP/KT ,cotton ,expression patterns ,fiber development ,stress ,Genetics ,QH426-470 - Published
- 2021
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27. GhGPAT12/25 Are Essential for the Formation of Anther Cuticle and Pollen Exine in Cotton (Gossypium hirsutum L.)
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Meng Zhang, Hengling Wei, Pengbo Hao, Aimin Wu, Qiang Ma, Jingjing Zhang, Hantao Wang, Xiaokang Fu, Liang Ma, Jianhua Lu, and Shuxun Yu
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GhGPAT12/25 ,cotton ,CRISPR/Cas9 ,male sterility ,anther cuticle ,pollen exine ,Plant culture ,SB1-1110 - Abstract
Glycerol-3-phosphate acyltransferases (GPATs), critical for multiple biological processes like male fertility, have been extensively characterized. However, their precise functions and underlying regulatory mechanism in cotton anther development are unclear. This research demonstrated the importance of GhGPAT12/25 (a paralogs pair on A12/D12 sub-chromosome of cotton) to regulate the degradation of tapetum, anther cuticle formation, and pollen exine development. GhGPAT12 and GhGPAT25 exhibited specifically detected transcripts in tapetum and pollen exine during the early anther developmental stages. GhGPAT12/25 are sn-2 glycerol-3-phosphate acyltransferases and can transfer the acyl group of palmitoyl-CoA to glycerol-3-phosphate (G3P). CRISPR/Cas9-mediated knockout identified the functional redundancy of GhGPAT12 and GhGPAT25. Knockout of both genes caused completely male sterility associated with abnormal anther cuticle, swollen tapetum, and inviable microspores with defective exine and irregular unrestricted shape. RNA-seq analysis showed that the loss of function of GhGPAT12/25 affects the processes of wax metabolic, glycerol monomer biosynthesis, and transport. Consistently, cuticular waxes were dramatically reduced in mutant anthers. Yeast one-hybrid system (Y1H), virus-induced gene silencing (VIGS), and dual-luciferase (LUC) assays illustrated that GhMYB80s are likely to directly activate the expression of GhGPAT12/25. This study provides important insights for revealing the regulatory mechanism underlying anther development in cotton.
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- 2021
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28. A Comprehensive Identification and Function Analysis of Serine/Arginine-Rich (SR) Proteins in Cotton (Gossypium spp.)
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Fei Wei, Pengyun Chen, Hongliang Jian, Lu Sun, Xiaoyan Lv, Hengling Wei, Hantao Wang, Tingli Hu, Liang Ma, Xiaokang Fu, Jianhua Lu, Shiyun Li, and Shuxun Yu
- Subjects
Gossypium hirsutum ,serine/arginine-rich proteins ,salt stress ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
As one of the most important factors in alternative splicing (AS) events, serine/arginine-rich (SR) proteins not only participate in the growth and development of plants but also play pivotal roles in abiotic stresses. However, the research about SR proteins in cotton is still lacking. In this study, we performed an extensive comparative analysis of SR proteins and determined their phylogeny in the plant lineage. A total of 169 SR family members were identified from four Gossypium species, and these genes could be divided into eight distinct subfamilies. The domain, motif distribution and gene structure of cotton SR proteins are conserved within each subfamily. The expansion of SR genes is mainly contributed by WGD and allopolyploidization events in cotton. The selection pressure analysis showed that all the paralogous gene pairs were under purifying selection pressure. Many cis-elements responding to abiotic stress and phytohormones were identified in the upstream sequences of the GhSR genes. Expression profiling suggested that some GhSR genes may involve in the pathways of plant resistance to abiotic stresses. The WGCNA analysis showed that GhSCL-8 co-expressed with many abiotic responding related genes in a salt-responding network. The Y2H assays showed that GhSCL-8 could interact with GhSRs in other subfamilies. The subcellular location analysis showed that GhSCL-8 is expressed in the nucleus. The further VIGS assays showed that the silencing of GhSCL-8 could decrease salt tolerance in cotton. These results expand our knowledge of the evolution of the SR gene family in plants, and they will also contribute to the elucidation of the biological functions of SR genes in the future.
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- 2022
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29. Genome-Wide Identification and Expression Pattern Analysis of the HAK/KUP/KT Gene Family of Cotton in Fiber Development and Under Stresses
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Xu Yang, Jingjing Zhang, Aimin Wu, Hengling Wei, Xiaokang Fu, Miaomiao Tian, Liang Ma, Jianhua Lu, Hantao Wang, and Shuxun Yu
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HAK/KUP/KT ,cotton ,expression patterns ,fiber development ,stress ,Genetics ,QH426-470 - Abstract
The potassium transporter family HAK/KUP/KT is a large group of proteins that are important in plant potassium transport and plays a crucial role in plant growth and development, especially in economic crops. Although HAK/KUP/KT genes have been identified in many species, research on these genes in cotton is still quite rare. In this study, in total, 21, 24, 45, and 44 HAK/KUP/KT genes were identified in Gossypium arboreum, Gossypium raimondii, Gossypium hirsutum, and Gossypium barbadense, respectively. Phylogenetic analysis showed that these genes were divided into four clusters. The G. hirsutum gene promoters contained diverse cis-regulatory elements, such as drought-responsive elements, low temperature-responsive elements, and other elements. The RNA-seq data and qRT-PCR results showed that HAK/KUP/KT genes had different expression patterns in fiber development. The qRT-PCR results of drought and NaCl treatment indicated that HAK/KUP/KT genes might play important roles in abiotic stress responses. These results will provide molecular insights into potassium transporter research in cotton.
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- 2020
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30. Assessing Reliability of Chinese Geotagged Social Media Data for Spatiotemporal Representation of Human Mobility
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Lingbo Liu, Ru Wang, Weihe Wendy Guan, Shuming Bao, Hanchen Yu, Xiaokang Fu, and Hongqiang Liu
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human mobility ,social media ,geotagged ,Sina Weibo ,Baidu Qianxi ,LBS ,Geography (General) ,G1-922 - Abstract
Understanding the space-time dynamics of human activities is essential in studying human security issues such as climate change impacts, pandemic spreading, or urban sustainability. Geotagged social media posts provide an open and space-time continuous data source with user locations which is convenient for studying human movement. However, the reliability of Chinese geotagged social media data for representing human mobility remains unclear. This study compares human movement data derived from the posts of Sina Weibo, one of the largest social media software in China, and that of Baidu Qianxi, a high-resolution human movement dataset from ‘Baidu Map’, a popular location-based service in China with 1.3 billion users. Correlation analysis was conducted from multiple dimensions of time periods (weekly and monthly), geographic scales (cities and provinces), and flow directions (inflow and outflow), and a case study on COVID-19 transmission was further explored with such data. The result shows that Sina Weibo data can reveal similar patterns as that of Baidu Qianxi, and that the correlation is higher at the provincial level than at the city level and higher at the monthly scale than at the weekly scale. The study also revealed spatial variations in the degree of similarity between the two sources. Findings from this study reveal the values and properties and spatiotemporal heterogeneity of human mobility data extracted from Weibo tweets, providing a reference for the proper use of social media posts as the data sources for human mobility studies.
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- 2022
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31. Genome-Wide Identification and Expression Analysis of the NHX (Sodium/Hydrogen Antiporter) Gene Family in Cotton
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Xiaokang Fu, Zhengying Lu, Hengling Wei, Jingjing Zhang, Xu Yang, Aimin Wu, Liang Ma, Meng Kang, Jianhua Lu, Hantao Wang, and Shuxun Yu
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Gossypium ,Na+/H+ antiporter protein ,gene expansion ,salt tolerance ,stress response ,Genetics ,QH426-470 - Abstract
The sodium/hydrogen antiporter (NHX) gene family with the Na+/H+ exchange protein domain is a transporter of sodium and hydrogen ions and plays an important role in the response of plants to salt stress. Studying the response of cotton to salt stress through comprehensive identification and analysis of NHX genes in several species and their roles in salt tolerance mechanisms is of great significance. In this study, 23, 24, 12, and 12 NHX genes were identified from Gossypium hirsutum (Gh), G. barbadense, G. arboreum and G. raimondii, respectively. Phylogenetic analysis showed that these genes were mainly divided into three clades with significant subcellular localization, namely, endosome (Endo-class), plasma membrane (PM-class) and vacuole (Vac-class). By analyzing the structure of NHX genes and proteins, each branch of the NHX gene family was found to be structurally conserved, and collinearity analysis showed that NHX genes were mainly expressed through whole genome and segmental duplication. The non-synonymous (Ka)/synonymous (Ks) values showed that the NHX gene family experienced strong purifying selection during long-term evolution. Cis-acting element analysis showed that the NHX gene family may be related to the regulation of abscisic acid (ABA) and methyl jasmonate (MeJA) hormones. Additionally, transcriptomic data analysis and qRT-PCR showed that GhNHXs exhibited different expression patterns in each tissue and under different salinities. These results provide an important reference for us to further understand and analyze the molecular regulation mechanism of cotton NHX genes.
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- 2020
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32. Dual Reproductive Cell-Specific Promoter-Mediated Split-Cre/LoxP System Suitable for Exogenous Gene Deletion in Hybrid Progeny of Transgenic Arabidopsis
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Chen Yang, Jia Ge, Xiaokang Fu, Keming Luo, and Changzheng Xu
- Subjects
Arabidopsis ,biosafety ,Cre/LoxP ,hybrid ,reproductive cell specificity ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Genetically modified (GM) crops possess some superior characteristics, such as high yield and insect resistance, but their biosafety has aroused broad public concern. Some genetic engineering technologies have recently been proposed to remove exogenous genes from GM crops. Few approaches have been applied to maintain advantageous traits, but excising exogenous genes in seeds or fruits from these hybrid crops has led to the generation of harvested food without exogenous genes. In a previous study, split-Cre mediated by split intein could recombine its structure and restore recombination activity in hybrid plants. In the current study, the recombination efficiency of split-Cre under the control of ovule-specific or pollen-specific promoters was validated by hybridization of transgenic Arabidopsis containing the improved expression vectors. In these vectors, all exogenous genes were flanked by two loxP sites, including promoters, resistance genes, reporter genes, and split-Cre genes linked to the reporter genes via LP4/2A. A gene deletion system was designed in which NCre was driven by proDD45, and CCre was driven by proACA9 and proDLL. Transgenic lines containing NCre were used as paternal lines to hybridize with transgenic lines containing CCre. Because this hybridization method results in no co-expression of the NCre and CCre genes controlled by reproduction-specific promoters in the F1 progeny, the desirable characteristics could be retained. After self-crossing in F1 progeny, the expression level and protein activity of reporter genes were detected, and confirmed that recombination of split-Cre had occurred and the exogenous genes were partially deleted. The gene deletion efficiency represented by the quantitative measurements of GUS enzyme activity was over 59%, with the highest efficiency of 73% among variable hybrid combinations. Thus, in the present study a novel dual reproductive cell-specific promoter-mediated gene deletion system was developed that has the potential to take advantage of the merits of GM crops while alleviating biosafety concerns.
- Published
- 2021
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33. Evaluation of Micro-Mechanism and High- and Low-Temperature Rheological Properties of Disintegrated High Volume Crumb Rubber Asphalt (DHVRA)
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Wei Li, Sen Han, Xiaokang Fu, and Ke Huang
- Subjects
modified asphalt ,high volume crumb rubber ,disintegrating agent ,micro-mechanism ,rheological characteristics ,Technology ,Electrical engineering. Electronics. Nuclear engineering ,TK1-9971 ,Engineering (General). Civil engineering (General) ,TA1-2040 ,Microscopy ,QH201-278.5 ,Descriptive and experimental mechanics ,QC120-168.85 - Abstract
The aims of this paper are to prepare disintegrated high volume crumb rubber asphalt (DHVRA) with low viscosity, good workability and low-temperature performance by adding disintegrating agent (DA) in the preparation process, and to further analyze the disintegrating mechanism and evaluated high-temperature and low-temperature rheological properties. To obtain DHVRA with excellent comprehensive performance, the optimum DA dosage was determined. Based on long-term disintegrating tests and the Fluorescence Microscopy (FM) method, the correlations between key indexes and crumb rubber (CR) particle diameter was analyzed, and the evaluation indicator and disintegrating stage division standard were put forward. Furthermore, Fourier transform infrared spectroscopy (FT-IR) and Gel Permeation Chromatography (GPC) was used to reveal the reaction mechanism, and the contact angle test method was adopted to evaluate the surface free energy (SFE). In addition, the high-temperature and low-temperature rheological properties were measured, and the optimum CR content was proposed. Results indicated that the optimum DA dosage was 7.5‰, and the addition of DA promoted the melt decomposition of CR, reduced the viscosity and improved the storage stability. The 135 °C rotational viscosity (RV) of DHVRA from mixing for 3 h could be reduced to 1.475 Pa·s, and the softening point difference was even less than 2 °C. The linear correlation between 135 °C RV and the diameter of CR particle in rubber asphalt system was as high as 0.968, and the viscosity decay rate (VDR) was used as the standard to divide the disintegrating process into a fast disintegrating stage, stable disintegrating stage and slight disintegrating stage. Compared to common rubber asphalt (CRA), DHVRA has an absorption peak at 960 cm−1 caused by trans olefin = C-H, and higher molecular weight and polar component of surface energy. Compared with CRA, although the high-temperature performance of DHVRA decreases slightly, the low-temperature relaxation ability can be greatly improved.
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- 2021
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34. A Novel Method of Interestingness Measures for Association Rules Mining Based on Profit
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Chunhua Ju, Fuguang Bao, Chonghuan Xu, and Xiaokang Fu
- Subjects
Mathematics ,QA1-939 - Abstract
Association rules mining is an important topic in the domain of data mining and knowledge discovering. Some papers have presented several interestingness measure methods; the most typical are Support, Confidence, Lift, Improve, and so forth. But their limitations are obvious, like no objective criterion, lack of statistical base, disability of defining negative relationship, and so forth. This paper proposes three new methods, Bi-lift, Bi-improve, and Bi-confidence, for Lift, Improve, and Confidence, respectively. Then, on the basis of utility function and the executing cost of rules, we propose interestingness function based on profit (IFBP) considering subjective preferences and characteristics of specific application object. Finally, a novel measure framework is proposed to improve the traditional one through experimental analysis. In conclusion, the new methods and measure framework are prior to the traditional ones in the aspects of objective criterion, comprehensive definition, and practical application.
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- 2015
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35. Using Social Media to Detect Outdoor Air Pollution and Monitor Air Quality Index (AQI): A Geo-Targeted Spatiotemporal Analysis Framework with Sina Weibo (Chinese Twitter).
- Author
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Wei Jiang, Yandong Wang, Ming-Hsiang Tsou, and Xiaokang Fu
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Medicine ,Science - Abstract
Outdoor air pollution is a serious problem in many developing countries today. This study focuses on monitoring the dynamic changes of air quality effectively in large cities by analyzing the spatiotemporal trends in geo-targeted social media messages with comprehensive big data filtering procedures. We introduce a new social media analytic framework to (1) investigate the relationship between air pollution topics posted in Sina Weibo (Chinese Twitter) and the daily Air Quality Index (AQI) published by China's Ministry of Environmental Protection; and (2) monitor the dynamics of air quality index by using social media messages. Correlation analysis was used to compare the connections between discussion trends in social media messages and the temporal changes in the AQI during 2012. We categorized relevant messages into three types, retweets, mobile app messages, and original individual messages finding that original individual messages had the highest correlation to the Air Quality Index. Based on this correlation analysis, individual messages were used to monitor the AQI in 2013. Our study indicates that the filtered social media messages are strongly correlated to the AQI and can be used to monitor the air quality dynamics to some extent.
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- 2015
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36. Fabric Defect Detection in Textile Manufacturing: A Survey of the State of the Art.
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Chao Li 0050, Jun Li, Yafei Li, Lingmin He, Xiaokang Fu, and Jingjing Chen
- Published
- 2021
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37. Creating Ensemble Classifiers with Information Entropy Diversity Measure.
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Jiangbo Zou, Xiaokang Fu, Lingling Guo, Chunhua Ju, and Jingjing Chen
- Published
- 2021
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38. Revealing the spatial co-occurrence patterns of multi-emotions from social media data.
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Dongyang Wang, Yandong Wang, Xiaokang Fu, Mingxuan Dou, Shihai Dong, and Duocai Zhang
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- 2023
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39. Understanding the topic evolution of scientific literatures like an evolving city: Using Google Word2Vec model and spatial autocorrelation analysis.
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Kai Hu 0005, Qing Luo, Kunlun Qi, Siluo Yang, Jin Mao, Xiaokang Fu, Jie Zheng, Huayi Wu, Ya Guo 0001, and Qibing Zhu
- Published
- 2019
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40. 融入区块链技术的大数据征信平台的设计与应用研究 (Design and Application of Big Data Credit Reporting Platform Integrating Blockchain Technology).
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Chunhua Ju, Jiangbo Zou, and Xiaokang Fu
- Published
- 2018
41. Functional analysis of the GhCYP94C1 gene in seed germination and flowering time of upland cotton
- Author
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MiaoMiao TIAN, Li AN, XiaoKang FU, HengLing WEI, Liang MA, JianHua LU, HanTao WANG, and ShuXun Yu
- Subjects
Pharmacology (medical) - Published
- 2022
42. Social media space provides public surveillance for suicide: 10-year study in Japan using advanced deep learning models (Preprint)
- Author
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Siqin Wang, Huan Ning, Huang Xiao, Yunyu Xiao, Mengxi Zhang, Fan Yang, Yukio Sadahiro, Yan Liu, Zhenlong Li, Tao Hu, Xiaokang Fu, Zi Li, and Ye Zeng
- Subjects
Health Informatics - Published
- 2023
43. Can social media space provide public surveillance for suicide? 10-year evidence from Japan (Preprint)
- Author
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Siqin Wang, Huan Ning, Huang Xiao, Yunyu Xiao, Mengxi Zhang, Fan Yang, Yukio Sadahiro, Yan Liu, Zhenlong Li, Tao Hu, Xiaokang Fu, Zi Li, and Ye Zeng
- Abstract
BACKGROUND Social media platforms have been increasingly used to express suicidal thoughts, feelings, and acts, raising public concerns over time. A large body of literature has explored the suicide risks identified by people’s expressions in social media space. However, there is less assertive to conclude that social media provides public surveillance for suicide without being able to align suicide risks detected in social media space with actual suicidal behaviours. Corroborating this alignment is a crucial foundation for suicide prevention and intervention through social media and for estimating and predicting suicide in countries with no reliable suicide statistics. OBJECTIVE This study aims to corroborate whether the suicide risks identified in social media space align with actual suicidal behaviours. This aim is achieved by tracking suicide risks detected by 62-million tweets posted in Japan over a 10-year period and assessing the locational and temporal alignment of such suicide risks with actual suicide behaviours, recorded in the national suicide statistics. METHODS This study utilizes a human-in-the-loop approach to identify suicide risk tweets posted in Japan in the period from January 2013 to December 2022. This approach involves keyword-filtered data mining, data scanning by human efforts, and data refinement via an advanced natural language processing model termed the Bidirectional Encoder Representations from Transformers. The tweets-identified suicide risks are then compared with actual suicide records in both temporal and spatial dimensions to validate if they are statistically correlated. RESULTS Twitter-identified suicide risks and actual suicide records are temporally correlated by month in the 10 years from 2013 to 2022 (correlation coefficient= 0.533; p CONCLUSIONS Social media platforms provide an anonymous space where people express their suicidal thoughts, ideation, and acts. Such expressions can serve as an alternative source to estimating and predicting suicide in countries without reliable suicide statistics. It can also provide real-time tracking of suicide risks, serving as the early warning for suicide committed. The identification of areas where suicide risks are highly concentrated is crucial for place-based mental health planning, enabling suicide prevention and intervention through social media in a spatially and temporally explicit manner. CLINICALTRIAL N/A
- Published
- 2023
44. A Dof Transcription Factor Ghdof1.7 Plays a Positive Regulatory Role Under Salinity Stress in Upland Cotton
- Author
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Yi Li, Miaomiao Tian, Zhen Feng, Hengling Wei, Jingjing Zhang, Jianhua Lu, Xiaokang Fu, Liang Ma, Shuxun Yu, and Hantao Wang
- Published
- 2023
45. Study on spatial distribution of coalbed methane contents in coal seams based on key interpolation points: an example from Shizhuang South block in, Shanxi Province, China
- Author
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Yang Sen, Xiaoming Ni, Xiaokang Fu, Bin Xu, and Wenlong Zhou
- Subjects
Fuel Technology ,General Chemical Engineering ,Energy Engineering and Power Technology ,General Chemistry ,Geotechnical Engineering and Engineering Geology - Published
- 2022
46. An evaluation method for types of low-production coalbed methane reservoirs and its application
- Author
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Xiaokang Fu, Xuebin Tan, Xiaoming Ni, and Wang Baoyu
- Subjects
Type of low-production CBM reservoir ,Mathematical model ,Computer simulation ,Petroleum engineering ,Coalbed methane ,Analytic hierarchy process ,Diffusion and seepage ,TK1-9971 ,Logging curve ,Permeability (earth sciences) ,Analytical hierarchy process ,General Energy ,Fluid dynamics ,Fracture (geology) ,Environmental science ,Desorption ,Electrical engineering. Electronics. Nuclear engineering ,Diffusion (business) - Abstract
At present, the macro-parameters such as critical desorption pressure, comprehensive diffusion coefficient, and permeability are commonly used to characterize the properties of a reservoir, and the productivity of coalbed methane (CBM) wells can be predicted through numerical simulation or established mathematical models, and the types of low-producing CBM reservoirs can be classified. However, low production from CBM wells is often caused by the weakness of one (or more) of desorption, diffusion, and seepage in CBM reservoirs, and the evaluation of a single link and macro-parametric characterization of reservoir properties cannot really ascertain the cause of the low production from a given CBM well.In the present work, the influences of pores and fracture structure, fluid flow dynamics and resistance on the desorption, diffusion, and seepage of CBM were considered from the perspective of system theory, and the evaluative parameter index system of low-productivity reservoirs was established. This avoids the one-sidedness of the evaluative results arising when only considering macro-parameters. New methods of obtaining the evaluative parameters pertaining to desorption, diffusion, and seepage are proposed: the methods include isothermal adsorption experiments, the use of logging curves, drainage data, mercury injection, and a classical mathematical model. These methods combined the data from experiments with in-situ data, and ensure the accuracy and practicability of the resulting evaluative parameters. On this basis, types of low-production reservoirs were classified using an analytic hierarchy process with multi-parameter superposition.The evaluative results pertaining to Shizhuang North block in the Qinshui Basin, Shanxi Province, China show that there are six types of low-yield reservoirs among the evaluative wells tested. Among them, diffusion is the main factor governing the low yield of CBM wells, followed by desorption and seepage. Herein, the reservoir constraint on CBM production is comprehensively evaluated, identifying the main controlling link affecting the low productivity of CBM wells, and laying a theoretical foundation for targeted transformation measures.
- Published
- 2021
47. Spatiotemporal characteristics and factor analysis of SARS-CoV-2 infections among healthcare workers in Wuhan, China
- Author
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Peixiao Wang, Tao Hu, Hongqiang Liu, Hui Ren, Xinyan Zhu, and Xiaokang Fu
- Subjects
Adult ,Male ,Microbiology (medical) ,China ,Physics - Physics and Society ,2019-20 coronavirus outbreak ,Health Personnel ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,education ,FOS: Physical sciences ,Physics and Society (physics.soc-ph) ,030501 epidemiology ,Healthcare worker infection ,Article ,Disease Outbreaks ,Geographical detector ,03 medical and health sciences ,Health personnel ,Spatio-Temporal Analysis ,Environmental health ,Health care ,Humans ,Medicine ,0303 health sciences ,SARS-CoV-2 ,030306 microbiology ,business.industry ,Central city ,COVID-19 ,Hospital level ,General Medicine ,Middle Aged ,Spatiotemporal pattern ,Occupational Diseases ,Infectious Diseases ,Infection sources ,Viral outbreak ,Female ,Factor analysis ,Factor Analysis, Statistical ,0305 other medical science ,business - Abstract
Studying the spatiotemporal distribution of SARS-CoV-2 infections among healthcare workers (HCWs) can aid in protecting them from exposure. Existing studies related to HCW infections have emphasized infection rates and protective measures. However, the spatiotemporal patterns and related external environmental factors of HCW infections remain unclear. To fill this gap, an open-source dataset of HCW diagnoses was provided, and the spatiotemporal distributions of SARS-CoV-2 infections among HCWs in Wuhan, China were explored. A geographical detector technique was then used to investigate the impacts of hospital level, type, distance from the infection source, and other external indicators of HCW infections. The results showed that the number of daily HCW infections over time in Wuhan followed a log-normal distribution, with and its mean observed on January 23, 2020 and a standard deviation of 10.8 days. The implementation of high-impact measures, such as the lockdown of the city, may have increased the probability of HCW infections in the short term, especially for HCWs in the outer ring of Wuhan. The infection of HCWs Wuhan exhibited clear spatial heterogeneity. The number of HCW infections was higher in the central city and lower in the outer city. Moreover, HCW infections displayed significant spatial autocorrelation and dependence. Factors analyses revealed that hospital level and type had an even greater impact on HCW infections; third-class and general hospitals closer to infection sources were correlated with especially high risks of infection. These findings can aid national epidemic prevention and control departments to understand the spatiotemporal distributions of viral transmission resulting in HCW infections, as well as external influencing factors, which can facilitate the protection of HCWs in China.
- Published
- 2021
48. Cytokinin signaling localized in phloem noncell‐autonomously regulates cambial activity during secondary growth of Populus stems
- Author
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Xuelian Du, Shuai Liu, Changzheng Xu, Huili Su, Keming Luo, and Xiaokang Fu
- Subjects
0106 biological sciences ,0301 basic medicine ,Cytokinins ,Physiology ,Secondary growth ,Plant Science ,Phloem ,Biology ,01 natural sciences ,03 medical and health sciences ,chemistry.chemical_compound ,heterocyclic compounds ,Cambium ,Transcription factor ,Gene knockdown ,fungi ,Histidine kinase ,food and beverages ,Cell biology ,Response regulator ,Populus ,030104 developmental biology ,chemistry ,Cytokinin ,Signal Transduction ,010606 plant biology & botany - Abstract
The regulation of cytokinin on secondary vascular development has been uncovered by modulating cytokinin content. However, it remains unclear how cytokinin enriched in developing secondary phloem regulates cambium activity in poplar. Here, we visualized the gradient distribution of cytokinin with a peak in the secondary phloem of poplar stem via immunohistochemical imaging, and determined the role of phloem-located cytokinin signaling during wood formation. We generated transgenic poplar harboring cytokinin oxidase/dehydrogenase (CKX)2, a gene encoding a cytokinin degrading enzyme, driven by the phloem-specific CLE41b promoter, indicating that the disruption of the cytokinin gradient pattern restricts the cambial activity. The RNA interference-based knockdown of the histidine kinase (HK) genes encoding cytokinin receptors specifically in secondary phloem significantly compromised the division activity of cambial cells, whereas the phloem-specific expression of a type-B response regulator (RR) transcription factor stimulated cambial proliferation, providing evidence for the noncell-autonomous regulation of local cytokinin signaling on the cambial activity. Moreover, the cambium-specific knockdown of HKs also led to restricted cambial activity, and the defects were aggravated by the reduced cytokinin accumulation. Our results showed that local cytokinin signaling in secondary phloem regulates cambial activity noncell-autonomously, and coordinately with its local signaling in cambium.
- Published
- 2021
49. GhGAI interacts with GhAP1 and regulates flowering pathway in upland cotton
- Author
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Zhen Feng, Qi Zhang, Yi Li, Pengbo Hao, Hengling Wei, Xiaokang Fu, Jianhua Lu, Liang Ma, Shuxun Yu, and Hantao Wang
- Subjects
Agronomy and Crop Science - Published
- 2023
50. Genome-wide identification of NF-YA gene family in cotton and the positive role of GhNF-YA10 and GhNF-YA23 in salt tolerance
- Author
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Xiaokang Fu, Liang Ma, Hengling Wei, Jianhua Lu, Shuxun Yu, Hantao Wang, Jingjing Zhang, and Qi Zhang
- Subjects
Cyclopentanes ,02 engineering and technology ,Acetates ,Biology ,Genes, Plant ,Gossypium raimondii ,Biochemistry ,Genome ,Chromosomes, Plant ,Conserved sequence ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Stress, Physiological ,Structural Biology ,Gene Duplication ,Gene family ,Gene silencing ,Gene Silencing ,Oxylipins ,Functional studies ,Nucleotide Motifs ,Selection, Genetic ,Promoter Regions, Genetic ,Molecular Biology ,Gene ,Conserved Sequence ,Phylogeny ,Plant Proteins ,030304 developmental biology ,Genetics ,Gossypium ,0303 health sciences ,Base Sequence ,Gene Expression Profiling ,Salt Tolerance ,General Medicine ,021001 nanoscience & nanotechnology ,Droughts ,Multigene Family ,Identification (biology) ,0210 nano-technology ,Genome, Plant ,Abscisic Acid - Abstract
Nuclear factor YA (NF-YA) genes play important roles in many biological processes, such as leaf growth, nitrogen nutrition, drought resistance, and salt stress. The functions of NF-YA genes in cotton have not been elucidated. The current study identified a total of 16, 16, 31, and 29 genes from Gossypium raimondii, G. arboretum, G. barbadense, and G. hirsutum, respectively. The NF-YA genes in cotton were phylogenetically classified into 4 groups. Analysis of gene structure, conserved motifs and multiple sequence alignments supported the evolutionary conservation of NF-YA family genes in cotton. Analysis of the expression patterns of GhNF-YAs in cotton suggested that GhNF-YAs play important roles in plant growth, development, and stress responses. The quantitative real-time PCR (qRT-PCR) validation of selected genes suggested that GhNF-YA genes are induced in response to salt, drought, ABA, and MeJA treatments. GhNF-YA genes may regulate salt and drought stress via the ABA or MeJA pathway. Silencing of GhNF-YA10 and GhNF-YA23 significantly reduced the salt tolerance of cotton seedlings, indicating that these genes participate in the regulation of the response of cotton to salt stress. These results establish a foundation for subsequent functional studies of the NF-YA gene family in cotton.
- Published
- 2020
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