Article
Plant Sciences
Ying Yang, Qiaoyu Huang, Xiaofei Wang, Jiaqi Mei, Anket Sharma, Durgesh Kumar Tripathi, Huwei Yuan, Bingsong Zheng
Summary: This study identified and characterized 23 ABCB genes (CcABCBs) in Chinese hickory. The expression profiles of auxin-related ABCBs were determined among tissues, under auxin-related phytohormone treatments, and during grafting. Many phytohormone-related cis-acting regulatory elements were detected on the promoters of CcABCB genes.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Article
Plant Sciences
Ying Yang, Jiayan Wang, Yan Xu, Farhat Abbas, Dongbin Xu, Shenchen Tao, Xiaoting Xie, Feng Song, Qiaoyu Huang, Anket Sharma, Luqing Zheng, Daoliang Yan, Xiaofei Wang, Bingsong Zheng, Huwei Yuan, Rongling Wu, Yi He
Summary: This study conducted the identification, structural characteristics, and gene expression analysis of the AUX/LAX gene family in Chinese hickory. Eight CcAUX/LAXs were identified in Chinese hickory, and they exhibited different expression profiles in different tissues and responded differently to drought and salt stress treatments. The study also found complex expression changes of these genes during Chinese hickory grafting. These findings provide valuable resources for further functional validation of CcAUX/LAXs and contribute to a better understanding of their potential regulatory functions during grafting and abiotic stress treatments in Chinese hickory.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Genetics & Heredity
Caiyun Li, Hongmiao Jin, Wei Zhang, Tao Qin, Xin Zhang, Zhenyang Pu, Zhengfu Yang, Kean-Jin Lim, Zhengjia Wang
Summary: The study identifies the role of long noncoding RNAs (lncRNAs) in the development of hickory female flowers. Through transcriptome analysis and prediction of interactions among miRNAs, lncRNAs, and genes, it is discovered that certain lncRNAs regulate the floral development by impacting key genes involved in hormone signaling pathways. This study provides new insights into the understanding of how lncRNAs function in the development of hickory female flowers.
FRONTIERS IN GENETICS
(2022)
Article
Plant Sciences
Jia-Hui Chen, Na Hou, Xv Xv, Da Zhang, Tong-Qiang Fan, Qi-Xiang Zhang, You-Jun Huang
Summary: This study investigated the changes of flavonoids in hickory during fruit development and identified core genes involved in flavonoid biosynthesis. Metabolite analysis revealed the presence of flavonoid-related metabolites. Transcriptome and metabolome analysis were combined to construct the regulatory pathway of flavonoid biosynthesis during hickory fruit development.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Hongmiao Jin, Zhengfu Yang, Jia Luo, Caiyun Li, Junhao Chen, Kean-Jin Lim, Zhengjia Wang
Summary: In this study, circRNAs in the flower buds of hickory were sequenced at three developmental stages, revealing several circRNAs involved in bud differentiation. These circRNAs were found to participate in multiple biological processes, including 46 circRNAs involved in flowering regulation. The preliminary results provided a theoretical basis for the involvement of circRNAs in flower development in hickory.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Agriculture, Multidisciplinary
Chunying Huang, Yan Li, Ketao Wang, Jianwei Xi, Haoyu Wang, Dongmei Zhu, Chenyu Jiang, Xiaolin Si, Duanshun Shi, Song Wang, Xiaobo Li, Jianqin Huang
Summary: Hickory (Carya cathayensis Sarg.), an important woody oil tree species with high nutritional value of its nuts, highlights the potential role of WRINKLED1 (WRI1) in hickory oil biosynthesis. Two hickory orthologs of WRI1 (CcWRI1A and CcWRI1B) were characterized, showing tissue-specific expression in developing embryos and the ability to restore oil content and expression of oil biosynthesis pathway genes in Arabidopsis wri1-1 mutant seeds.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Plant Sciences
C. J. Zhuang, Q. W. Wang, Q. Q. Wu, Z. L. Qiu, B. C. Xu, C. Q. Zhang
Summary: The study identified five fungal pathogens associated with tree trunk cankers on Chinese hickory trees, providing essential information for the understanding and management of this disease. The fastest-growing species on potato dextrose agar was Lasiodiplodia theobromae, while the slowest was Botryosphaeriaceae corticis. Spore germination for all species was optimal at 30 degrees Celsius, with L. theobromae being the most virulent.
Article
Chemistry, Applied
Fatima-ezzahra Ettoumi, Ruyuan Zhang, Tarun Belwal, Miral Javed, Yanqun Xu, Li Li, Lv Weide, Zisheng Luo
Summary: This study utilized nanobubbles as a green method to assist ionic liquid in extracting polyphenols from Carya cathayensis Sarg. husk. The IL-NBs extract showed higher antioxidant activity and polyphenol yields compared to common solutions, with nanobubbles causing morphological destruction of the husk powder. It revealed a more efficient polyphenol extraction method based on green nanotechnology.
Article
Food Science & Technology
Qing Li, Lu Wang, Meiyu Zheng, Hanyu Lu, Yinying Liu, Yangguang Wang, Shengmin Lu
Summary: Microencapsulation of hickory oil using beta-cyclodextrin or porous starch as wall materials can significantly improve its stability. Beta-cyclodextrin microcapsules showed superior storage performance compared to porous starch microcapsules, especially in terms of thermal and oxidative stability.
Article
Environmental Sciences
Daoliang Yan, Feng Song, Zhen Li, Anket Sharma, Xiaoting Xie, Tingting Wu, Xiaofei Wang, Yi He, Jiabao Chen, Qiaoyu Huang, Lu Zhao, Rongling Wu, Shihui Niu, Huwei Yuan, Bingsong Zheng
Summary: The study showed that spraying ASIT can increase the leaf mass per area and chlorophyll content of grafted hickory seedlings. ASIT treatment positively affected the Rubisco content and photosynthetic rate of seedlings grown under shading conditions, especially on the 45th day of treatment, with significant interaction effects between ASIT application and different shade treatments.
Article
Food Science & Technology
Fujie Yan, Qingqing Wang, Jialuo Teng, Fenghua Wu, Zhiping He
Summary: The crude protein powder from Carya cathayensis Sarg meal can be enzymatically hydrolyzed to produce low molecular weight peptides, which have protective effects on hepatocytes and can reduce oxidative stress. This method is simple, environmentally friendly, and cost-effective, and can be used to produce bioactive peptides for nutraceutical products and food preservation.
CURRENT RESEARCH IN FOOD SCIENCE
(2023)
Article
Forestry
Chunying Huang, Yan Li, Ketao Wang, Jianwei Xi, Yifan Xu, Junyan Hong, Xiaolin Si, Hongyu Ye, Shiheng Lyu, Guohua Xia, Jianhua Wang, Peipei Li, Yulin Xing, Yige Wang, Jianqin Huang
Summary: Hickory is a nut-bearing deciduous tree with a high oil content in its embryo. This study explored the molecular mechanism of high oil accumulation in hickory embryos. Transcriptome and proteome analysis identified genes and proteins involved in lipid metabolism, which showed the highest expression levels at 95 days after pollination. Furthermore, the co-regulatory network of lipid metabolism was constructed, and a core transcription factor WRI1 was identified.
Article
Agriculture, Multidisciplinary
Qing-li Han, Bai-xue Long, Xue-jun Yan, Wu Wang, Feng-ru Liu, Xue Chen, Fei Ma
Summary: This study assessed the feasibility of using acoustic vibration signals obtained from a homemade device as a non-destructive technology for identifying moldy kernels of in-shell hickory nuts (MK-IHNs). Twenty-two acoustic features were extracted from time-domain and frequency-domain signals to establish a model for classifying MK-IHNs and healthy kernels of in-shell hickory nuts (HK-IHNs). The optimized LIB support vector machine (Lib-SVM) model, based on a combination of time-domain and frequency-domain features, achieved an accuracy of 91.67% for identifying MK-IHNs. Physical parameters of hickory nuts, such as weight and bulk density, showed significant correlations with most of the acoustic features (P < 0.05). Additionally, the microstructures of HK-IHN and MK-IHN shells were visibly different, both on the outside surfaces and cross-sections. This highlights the importance of hickory nuts' physical forms and structures in developing a reliable model for identifying MK-IHNs using acoustic vibration technology. Satisfactory results demonstrated that the combination of acoustic vibration technology and Lib-SVM method can be a feasible approach for non-destructive damage identification of MK-IHNs.
COMPUTERS AND ELECTRONICS IN AGRICULTURE
(2023)
Article
Chemistry, Applied
Xizhe Fu, Di Wang, Tarun Belwal, Yanqun Xu, Li Li, Zisheng Luo
Summary: Combining natural deep eutectic solvent with pulse-ultrasonication technique demonstrated significant synergistic effect and high efficiency in extracting phenolic compounds from Carya cathayensis Sarg. peels. The development and validation of a second-order kinetic model further confirmed the synergistic effect and influence during extraction.
Article
Biotechnology & Applied Microbiology
Xiao-Hui Bai, Qi Yao, Genshan Li, Guan-Xiu Guan, Yan Fan, Xiufeng Cao, Hong-Guang Ma, Mei-Man Zhang, Lishan Fang, Aijuan Hong, Dacai Zhai
Summary: Carya cathayensis is an important nut tree in China, and root rot disease can cause reduced yields and economic losses. The composition and diversity of bacterial communities in C. cathayensis are associated with the development of root rot, and our study provides theoretical guidance for pathogen isolation and disease control.
JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Biochemical Research Methods
Qiang Kang, Jun Meng, Jun Cui, Yushi Luan, Ming Chen
Article
Biochemistry & Molecular Biology
Xinjian Yu, Siqi Lai, Hongjun Chen, Ming Chen
HUMAN MOLECULAR GENETICS
(2020)
Article
Multidisciplinary Sciences
Jingjing Wang, Yuriy L. Orlov, Xue Li, Yincong Zhou, Yongjing Liu, Chunhui Yuan, Ming Chen
Summary: This study explored the role of epigenetic modifications in regulating gene expression and functional divergence following gene duplication in plants. The analysis revealed that duplicate genes in Arabidopsis exhibit more similar histone modification patterns than single-copy genes, and the evolution of histone marks is linked to coding sequence divergence and expression divergence. Furthermore, duplicate genes with distinct functions show greater divergence in histone modification, while higher expression divergence is associated with mutations in chromatin modifiers.
Article
Cell Biology
Jingjing Wang, Huiyu Sun, Mengmeng Jiang, Jiaqi Li, Peijing Zhang, Haide Chen, Yuqing Mei, Lijiang Fei, Shujing Lai, Xiaoping Han, Xinhui Song, Suhong Xu, Ming Chen, Hongwei Ouyang, Dan Zhang, Guo-Cheng Yuan, Guoji Guo
Summary: Cell types are the basic building units of multicellular life, showing both conservation and divergence during evolution. By analyzing single-cell RNA-seq data, a cross-species cell-type evolutionary hierarchy was constructed, revealing muscle and neuron cells as conserved types. Furthermore, a cross-species transcription factor repertoire was identified to specify major cell categories.
Article
Biology
Fei Liu, George Assaf, Ming Chen, Monika Heiner
Summary: This paper discusses the challenges and requirements of whole-cell modeling, categorizing them into three dimensions: heterogeneous biochemical networks, uncertainties in components, and representation of cell structure. Using different classes of Petri nets to address these requirements, a Petri nets-based framework for whole-cell modeling is proposed, offering a feasible modeling approach that meets multiple requirements and provides a graphical, modular, and hierarchical modeling tool.
Article
Cell & Tissue Engineering
Wei Shan, Qin Yu, Yan Long, Qian Luo, Honghu Li, Yingli Han, Yulin Xu, Shan Fu, Xiangjun Zeng, Cong Wei, Yang Gao, Xiaoqing Li, Xia Li, Lifei Zhang, Lizhen Liu, Ming Chen, Pengxu Qian, He Huang
Summary: This study established an in vitro differentiation system that successfully generated hematopoietic cells with in vivo hematopoietic reconstitution potential from mouse PSCs. The combination of 3D induction system and OP9 stromal cell coculture yielded c-kit(+) cells with superior repopulating activity.
STEM CELL RESEARCH & THERAPY
(2021)
Article
Cell Biology
Zhen Sun, Hua Yu, Jing Zhao, Tianyu Tan, Hongru Pan, Yuqing Zhu, Lang Chen, Cheng Zhang, Li Zhang, Anhua Lei, Yuyan Xu, Xianju Bi, Xin Huang, Bo Gao, Longfei Wang, Cristina Correia, Ming Chen, Qiming Sun, Yu Feng, Li Shen, Hao Wu, Jianlong Wang, Xiaohua Shen, George Q. Daley, Hu Li, Jin Zhang
Summary: LIN28 plays important roles in embryo development, stem cell differentiation, and tumorigenesis. Its loss can lead to nucleolar stress and activation of a transcriptional program similar to the 2-cell stage, revealing novel functions in pluripotent stem cells.
Article
Genetics & Heredity
Nann Miky Moh Moh, Peijing Zhang, Yujie Chen, Ming Chen
Summary: This study is the first to provide information on non-coding RNAs (ncRNAs) of mango, identifying around 100 miRNAs and over 7,000 temperature-responsive lncRNAs, and characterizing their potential functions and target genes. The newly identified mango ncRNAs are suggested to play roles in various biological and metabolic pathways, including plant growth, pathogen defense, and stress response, with lncRNAs potentially acting as decoys or sponges for miRNAs. Further wet lab experiments are needed to investigate the specific functions of mango ncRNAs.
FRONTIERS IN GENETICS
(2021)
Article
Genetics & Heredity
Hua Yu, Lu Lu, Ming Chen, Chen Li, Jin Zhang
Summary: KDDANet is a novel computational tool for identifying hidden genes mediating Known Drug-Disease Association, showing competitive performance. Case studies on Alzheimer's disease and obesity revealed the mechanistic relevance of KDDANet predictions. Additionally, KDDANet can discover shared genes mediating multiple KDDAs.
NPJ GENOMIC MEDICINE
(2021)
Article
Biochemical Research Methods
Xiaotian Hu, Cong Feng, Yincong Zhou, Andrew Harrison, Ming Chen
Summary: DeepTrio is a sequence-based approach for predicting protein-protein interaction (PPI) using multiple parallel masked convolutional neural networks. Experimental evaluations show that DeepTrio outperforms several state-of-the-art methods in terms of various quality metrics, and it provides additional insights into the contribution of each input neuron to the prediction results.
Article
Multidisciplinary Sciences
Hua Yu, Zhen Sun, Tianyu Tan, Hongru Pan, Jing Zhao, Ling Zhang, Jiayu Chen, Anhua Lei, Yuqing Zhu, Lang Chen, Yuyan Xu, Yaxin Liu, Ming Chen, Jinghao Sheng, Zhengping Xu, Pengxu Qian, Cheng Li, Shaorong Gao, George Q. Daley, Jin Zhang
Summary: The nucleolus plays a crucial role in regulating the fate transition of mouse embryonic stem cells to 2 cell-stage embryo-like cells through maintaining nucleolar integrity and reshaping the 3D chromatin structure. Additionally, rRNA biogenesis is essential for the transition from 2-cell to 4-cell stage during murine pre-implantation embryo development.
NATURE COMMUNICATIONS
(2021)
Review
Biochemical Research Methods
Md Asif Ahsan, Yongjing Liu, Cong Feng, Yincong Zhou, Guangyuan Ma, Youhuang Bai, Ming Chen
Summary: The COVID-19 pandemic, caused by SARS-CoV-2, poses an unprecedented threat to public health globally. With no approved drugs or vaccines available, urgent research is needed to understand the virus's pathogenesis and develop effective treatments, requiring collaboration and integration of molecular information from researchers worldwide.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Cong Feng, Min Dai, Yongjing Liu, Ming Chen
Summary: The study introduces a new computational approach called RepLoc for efficient identification of repetitive sequences in the genome, revealing potential relationships between sequence repetitiveness and genome structures.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Mathematical & Computational Biology
Md Asif Ahsan, Yongjing Liu, Cong Feng, Ralf Hofestaedt, Ming Chen
Summary: The ongoing threat of COVID-19 has led to the generation of vast amounts of data regarding the novel coronavirus SARS-CoV-2. To facilitate researchers in accessing these resources and accelerating clinical research, an integrated web portal called OverCOVID has been developed, providing a one-stop platform for accessing publicly available webservers, databases, and tools associated with SARS-CoV-2.
JOURNAL OF INTEGRATIVE BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Jingjing Wang, Qi Chen, Wenyi Wu, Yujie Chen, Yincong Zhou, Guoji Guo, Ming Chen
Summary: Nutrient stress is the most important environmental stress that limits plant growth, and this study identified and characterized lncRNAs under seven different nutrient stress conditions in Arabidopsis thaliana. It was found that lncRNAs are more sensitive to nutrient stress and exhibit stress-specific expression patterns. The study also constructed ceRNA network and lncRNA-mRNA co-expression network to explore the potential function of lncRNAs under nutrient stress conditions.
FUNCTIONAL & INTEGRATIVE GENOMICS
(2021)