Article
Biotechnology & Applied Microbiology
Chongyang Ma, Kai Yan, Zisong Wang, Qiuyun Zhang, Lianyin Gao, Tian Xu, Jiayang Sai, Fafeng Cheng, Yuqiong Du
Summary: The study revealed a complex relationship between hypertension and NAFLD, identifying shared genes and potential mechanisms. The genes were associated with inflammatory, metabolic, and endocrine signals, suggesting a multi-target therapeutic strategy for future clinical research.
Article
Genetics & Heredity
Basdeo Kushwaha, Neha Srivastava, Murali S. Kumar, Ravindra Kumar
Summary: This study aimed to understand the interaction of the brain-gonad system in Clarias magur reproduction by analyzing differentially expressed genes (DEG). Thirteen key genes in female brain & ovary and twelve key genes in male brain & testis were identified based on network analysis. Functional annotation revealed their involvement in important reproduction-related pathways. This study provides insights into the interaction between the brain and gonads in the regulation of Clarias magur reproduction through a protein-protein interaction network.
Article
Biochemistry & Molecular Biology
Chunyu Yu, Yunzhi Lang, Chao Hou, Ence Yang, Xianwen Ren, Tingting Li
Summary: Liquid-liquid phase separation (LLPS) is an important mechanism in the formation of biomolecular condensates. This study integrated a human protein-protein interaction network (HPIN) and mapped phase-separated proteins into it. The analysis revealed differences in network topology between phase-separated proteins and others, and showed that affinity purification mass spectrometry (AP-MS) is more effective than the yeast-two-hybrid system (Y2H) in detecting protein-protein interactions (PPIs) in phase separation-driven condensates.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Genetics & Heredity
Jessica Schuster, George A. Tollefson, Valeria Zarate, Anthony Agudelo, Joan Stabila, Ashok Ragavendran, James Padbury, Alper Uzun
Summary: This study used whole exome sequencing and network analysis to identify shared gene networks associated with severe preeclampsia, as well as specific genes related to the pathogenic mechanisms of preeclampsia.
FRONTIERS IN GENETICS
(2022)
Article
Biochemical Research Methods
L. F. Signorini, T. Almozlino, R. Sharan
Summary: ANAT3.0 is a powerful Cytoscape plugin that offers updated PPI network databases and a new machine-learning layer to better reconstruct known signaling pathways.
BMC BIOINFORMATICS
(2021)
Article
Computer Science, Artificial Intelligence
Peizhen Bai, Filip Miljkovic, Bino John, Haiping Lu
Summary: DrugBAN is a deep bilinear attention network framework that explicitly learns the local interactions between drugs and targets, and adapts to out-of-distribution data. It achieves the best performance on three benchmark datasets compared to five state-of-the-art baseline models. The visualized bilinear attention map provides interpretable insights from prediction results.
NATURE MACHINE INTELLIGENCE
(2023)
Article
Biochemistry & Molecular Biology
Rong Liu, Guangxi Yang, Min Bao, Zhongmei Zhou, Xiaoyun Mao, Wenjing Liu, Xiaoyan Jiang, Di Zhu, Xinle Ren, Jian Huang, Ceshi Chen
Summary: This study identifies STAMBPL1 as a deubiquitinase of MKP-1 in breast cancer cells, which stabilizes MKP-1 protein by deubiquitination. Depletion of STAMBPL1 and MKP-1 increases breast cancer sensitivity to cisplatin and activates the JNK signaling pathway. These findings suggest that the STAMBPL1/MKP-1 axis could be a potential therapeutic target in breast cancer.
Article
Cell Biology
Shuai Wang, Zongyang Qiu, Yingnan Hou, Xiya Deng, Wei Xu, Tingting Zheng, Peihan Wu, Shaofang Xie, Weixiang Bian, Chong Zhang, Zewei Sun, Kunpeng Liu, Chao Shan, Aifu Lin, Shibo Jiang, Youhua Xie, Qiang Zhou, Lu Lu, Jing Huang, Xu Li
Summary: This study found that AXL may serve as a novel receptor for SARS-CoV-2, playing an important role in promoting viral infection of the human respiratory system. AXL expression level is closely correlated with SARS-CoV-2 S level and could be a potential target for future clinical intervention strategies.
Review
Biochemistry & Molecular Biology
E. C. Dacol, S. Wang, Y. Chen, A. P. Lepique
Summary: Loss of function of tumor suppressor proteins in cancer cells is often the result of genetic mutations. Protein Phosphatase 2A (PP2A) is a tumor suppressor that is inactivated by endogenous inhibitors, leading to sustained activation of mitogenic signaling pathways. One of these inhibitors, SET, interacts with PP2A and is associated with high expression in various cancers, suggesting disruption of SET-PP2A interaction as a potential therapeutic strategy.
BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER
(2021)
Article
Multidisciplinary Sciences
Emily Z. Guo, Jorge E. Galan
Summary: Type III secretion systems are multiprotein molecular machines essential for the virulence of bacterial pathogens. The injectisome mediates the delivery of bacterially encoded proteins into eukaryotic target cells. The structure of the needle tip complex and its interaction with the needle filament are crucial for the translocation of effector proteins.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Renee L. Hastings, Steven Boeynaems
Summary: Protein phase separation is a novel paradigm in cell biology that provides insights into how cells compartmentalize biochemical reactions and encode function in liquid-like assemblies. This understanding offers immense opportunities for designing and sculpting biological matter to create new functionalized materials and tools for synthetic biology. Studies suggest that designer condensates have potential applications in industry and medicine.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Cell Biology
Hai-Liang Zhang, Bing-Xin Hu, Zhi-Ling Li, Tian Du, Jia-Lu Shan, Zhi-Peng Ye, Xiao-Dan Peng, Xuan Li, Yun Huang, Xian-Ying Zhu, Yu-Hong Chen, Gong-Kan Feng, Dajun Yang, Rong Deng, Xiao-Feng Zhu
Summary: Through CRISPR-Cas9 and kinase inhibitor screening, Zhang et al. found that PKC beta II phosphorylates and activates ACSL4 to enhance polyunsaturated fatty acid-containing lipid biosynthesis, thereby promoting accumulation of lipid peroxidation and ferroptosis.
NATURE CELL BIOLOGY
(2022)
Article
Engineering, Environmental
Jinpeng Han, Xiaocui Guo, Feng Li, Dayong Yang
Summary: The compartmentalization and rough surface of the nucleus are proposed to facilitate biosynthesis. Microgels similar to the nucleus were created with controllable roughness, and it was found that rough microgels showed higher protein yield and initial expression rate. Mechanism investigation revealed that rough microgels with higher specific surface area and multi-modal pore-size distribution compressed more genes and improved the enzyme turnover rate for efficient biosynthesis.
CHEMICAL ENGINEERING JOURNAL
(2022)
Review
Biochemistry & Molecular Biology
Shutang Tan, Christian Luschnig, Jiri Friml
Summary: The plant hormone auxin is central to plant growth and development, with protein phosphorylation emerging as a crucial post-translational modification type regulating auxin output. This review comprehensively discusses the genetics, biochemistry, and cell biology of kinases and phosphatases involved in auxin action, providing insights into the mechanisms of developmental auxin responses and future directions for integrating protein phosphorylation control into the molecular auxin network.
Review
Cardiac & Cardiovascular Systems
Abhijeet Rajendra Sonawane, Elena Aikawa, Masanori Aikawa
Summary: Cardiovascular diseases (CVD) affect millions of people worldwide and can be studied using multiomics biomedical data and the approaches of systems biology and network medicine to understand their causes, mechanisms, and potential treatments.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2022)