Article
Biotechnology & Applied Microbiology
Jingjing Li, Yifei Gou, Jiarui Yang, Lingxuan Zhao, Bin Wang, Tong Hao, Jinsheng Sun
Summary: In this study, a genome-scale metabolic network model of Eriocheir sinensis was reconstructed, and its optimal nutrient requirements were predicted. Suggestions for feed improvement were provided based on the simulation results. This study is of great importance in improving the yield and economic value of E. sinensis.
Article
Multidisciplinary Sciences
Changyue Yu, Zhiwei Huang, Yingkai Xu, Baoli Zhang, Yingdong Li
Summary: This study investigated the mechanisms of miRNA regulation of circadian rhythms in the Chinese mitten crab. The results showed that 23 known miRNAs were differentially expressed depending on the time of day, and the putative target genes for these miRNAs were significantly enriched in the immune response and endocrine-related pathways. These findings suggest that miRNAs play a role in regulating specific physiological functions in the Chinese mitten crab under circadian cycles.
SCIENTIFIC REPORTS
(2023)
Article
Biotechnology & Applied Microbiology
Betuel Kaynar, Dilara Uzuner, Tunahan Cakir
Summary: In this study, a genome-scale metabolic network model, iPc610, was reconstructed for P. copri DSM 18205 through an intensive manual curation process. The model consists of 1737 metabolic reactions controlled by 610 genes. The prediction performance of iPc610 was validated with experimental data, showing reliable predictions of by-product secretions under anaerobic conditions. Gene essentiality simulations identified 70 essential genes, which can be used as candidate targets in future studies to restore dysregulated gut microbiota composition in various diseases.
BIOCHEMICAL ENGINEERING JOURNAL
(2023)
Article
Environmental Sciences
Tianyu Wang, Chen Yang, Shuang Zhang, Liyan Rong, Xiaofei Yang, Zhaoxia Wu, Wentao Sun
Summary: This study investigated the metabolic changes and stress damage in juvenile Eriocheir sinensis induced by exposure to varying concentrations of ammonia, providing insights into the molecular mechanisms underlying ammonia toxicity and adaptive responses in the species.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Article
Plant Sciences
Nan Xu, Qiyuan Yang, Xiaojing Yang, Mingqi Wang, Minliang Guo
Summary: This study utilized a genome-scale metabolic model to investigate the metabolic characteristics of Agrobacterium tumefaciens and found differences in metabolic activity in different ecological niches. By integrating transcriptome data under tumor conditions, significant changes in metabolic pathways were identified.
MOLECULAR PLANT PATHOLOGY
(2021)
Article
Multidisciplinary Sciences
Hao Wang, Jonathan L. Robinson, Pinar Kocabas, Johan Gustafsson, Mihail Anton, Pierre-Etienne Cholley, Shan Huang, Johan Gobom, Thomas Svensson, Mattias Uhlen, Henrik Zetterberg, Jens Nielsen
Summary: Genome-scale metabolic models (GEMs) are extensively used for analyzing mechanisms of human diseases and metabolic disorders. A unified platform of GEMs covering five major model animals was presented, providing comprehensive metabolic network coverage and revealing a potential biomarker for early diagnosis of Alzheimer's disease through integrative analysis of RNA-sequencing and proteomics data.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Marine & Freshwater Biology
Tianyu Wang, Chen Yang, Tingting Zhang, Hanling Liang, Yichao Ma, Zhaoxia Wu, Wentao Sun
Summary: This study explored the toxic responses in the hepatopancreas of juvenile E. sinensis exposed to ammonia-N, showing that ammonia stress activated the immune defense system, upregulated detoxification genes, and accelerated glycogen degradation. Additionally, the tricarboxylic acid cycle and amino acid consumption were enhanced for energy supply to cope with ammonia stress.
AQUATIC TOXICOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Andrew Walakira, Damjana Rozman, Tadeja Rezen, Miha Mraz, Miha Moskon
Summary: Omics data can be integrated into a reference model using different model extraction methods (MEMs) to generate context-specific genome-scale metabolic models (GEMs). The choice of MEM, thresholding rule, and threshold presents a challenge, with differences in model size and variability explained by different MEMs observed. Among the MEMs tested, FASTCORE was found to capture the most true variability in the data, particularly related to gender differences.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biotechnology & Applied Microbiology
Defei Liu, Zixiang Xu, Jingen Li, Qian Liu, Qianqian Yuan, Yanmei Guo, Hongwu Ma, Chaoguang Tian
Summary: In this study, a manually curated genome-scale metabolic model iDL1450 for Myceliophthora thermophila was constructed, and its carbon and nitrogen source utilization was validated. Additionally, metabolism analysis was performed using iDL1450 integrated with transcriptomics data, providing new insights into the metabolism of thermophilic fungi.
BIOTECHNOLOGY AND BIOENGINEERING
(2022)
Article
Oncology
Seungyoon Nam, Yongmin Lee
Summary: Gastric cancer is a deadly cancer with different histological subtypes. This study used transcriptome analysis to identify differential metabolic pathways between the diffuse and intestinal subtypes of gastric cancer, including cholesterol homeostasis, xenobiotic metabolism, fatty acid metabolism, the MTORC1 pathway, and glycolysis.
Article
Multidisciplinary Sciences
Jun Wang, Xiaowen Chen, Xin Hou, Jingan Wang, Wucheng Yue, Shu Huang, Gangchun Xu, Jizhou Yan, Guoqing Lu, Michael Hofreiter, Chenhong Li, Chenghui Wang
Summary: This study presents the chromosome-level genome of the Chinese mitten crab Eriocheir sinensis and transcriptome data during limb regeneration. The findings reveal novel genetic pathways involved in arthropod limb regeneration and provide valuable resources for comparative and regeneration studies.
Article
Fisheries
Libo Hou, Lei Zhu, Xianghui Kong, Yinyue Lu, Wen Wang, Wei Gu, Li Wang, Qingguo Meng
Summary: In this study, the impact of hypoxia on Chinese mitten crab Eriocheir sinensis hemocytes was investigated using iTraq labeling and LC-MS/MS analysis. The results showed significant changes in protein expression, involving various pathways and biological processes. The study also analyzed the increased activity of antioxidant enzymes under hypoxia stress.
AQUACULTURE REPORTS
(2021)
Article
Environmental Sciences
Yanan Yang, Yuanfeng Xu, Peng Zhang, Zhaoxia Cui, Chenchang Bao
Summary: The CHH superfamily neuropeptides, which include CHH, MIH, VIH/GIH, and MOIH, are involved in various biological activities such as metabolism, molting, reproduction, and osmotic regulation. The discovery of ITP in insects expanded the members of CHHs.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Fisheries
Nan Mo, Dan-dan Zhu, Jia-xin Liu, Tianyi Feng, Zhaoxia Cui
Summary: The air-exposure stress (AES) in aquacultural practices can affect the survival rate of cultured animals by inducing adjustments in energy utilization, respiration, antioxidant production, and immune activity. A combination of metabolomic and transcriptomic analysis was used to study Chinese mitten crabs' metabolic responses to AES, revealing an increase in carbohydrate and lipid metabolism-related metabolites and changes in gene expression. Lowering temperature was found to alleviate the impacts of AES by depressing metabolic rates, and sexual dimorphism in lipid metabolism in Eriocheir sinensis was demonstrated.
Article
Fisheries
Libo Hou, Jie Du, Qiulin Ren, Lei Zhu, Xianliang Zhao, Xianghui Kong, Wei Gu, Li Wang, Qingguo Meng
Summary: By applying label-free quantitative liquid chromatography with tandem mass spectrometry proteomics, the study identified 950 lysine ubiquitination sites and 803 ubiquitination peptides on 458 proteins after S. eriocheiris infection. Bioinformatics analysis of ubiquitination different proteins indicated the involvement of various biological processes and pathways in the interaction between S. eriocheiris and host cell.
FISH & SHELLFISH IMMUNOLOGY
(2022)