Article
Biochemistry & Molecular Biology
Jingjing Jin, Peng Lu, Yalong Xu, Jiemeng Tao, Zefeng Li, Shuaibin Wang, Shizhou Yu, Chen Wang, Xiaodong Xie, Junping Gao, Qiansi Chen, Lin Wang, Wenxuan Pu, Peijian Cao
Summary: The emergence of single-cell sequencing has revolutionized transcriptomic and genomic research. The lack of a comprehensive database of cell markers for plant research community has been addressed by the development of PCMDB, providing a valuable resource for researchers to annotate cell types and predict the biological function of individual cells.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Plant Sciences
Jorge Xool-Tamayo, Yahaira Tamayo-Ordonez, Miriam Monforte-Gonzalez, Jose Armando Munoz-Sanchez, Felipe Vazquez-Flota
Summary: The synthesis of benzylisoquinoline alkaloids sanguinarine and berberine in Argemone mexicana was monitored during early stages of hypocotyl and seedling development, revealing distinct patterns of accumulation. Sanguinarine increased until cotyledon unfurling, while berberine accumulation required the formation of cotyledonary leaves. The study suggests that alkaloid tissue distribution patterns are established early in development and may involve transport systems.
Article
Pharmacology & Pharmacy
Naveen Kumar Velayutham, Tamilanban Thamaraikani, Shadma Wahab, Mohammad Khalid, Gobinath Ramachawolran, Shahabe Saquib Abullais, Ling Shing Wong, Mahendran Sekar, Siew Hua Gan, Angel Jemima Ebenezer, Mrinalini Ravikumar, Vetriselvan Subramaniyan, Nur Najihah Izzati Mat Rani, Yuan Seng Wu, Srikanth Jeyabalan
Summary: This study evaluated the regulatory effects of stylopine on the VEGFR-2 signaling pathway and its anti-tumor effect on human MG-63 osteosarcoma cells. In vitro experiments showed that stylopine inhibited cell proliferation, induced mitochondrial membrane damage and apoptosis in MG-63 cells, and suppressed cell migration and VEGFR2 expression induced by VEGF-165. The findings suggest that stylopine has the potential to regulate VEGFR2 and may serve as a new drug candidate for the treatment of bone cancer in the future.
FRONTIERS IN PHARMACOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Chen Cao, Mengting Shao, Chunman Zuo, Devin Kwok, Lin Liu, Yuli Ge, Zilong Zhang, Feifei Cui, Mingshuai Chen, Rui Fan, Yijie Ding, Hangjin Jiang, Guishen Wang, Quan Zou
Summary: Rare variants are important for genetic causes of complex traits, but there is currently no systematic collection of these associations. This study presents the Rare Variant Association Repository (RAVAR), which collects a large number of rare variant associations and provides an interactive interface with search functionality.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
James T. Payne, Timothy R. Valentic, Christina D. Smolke
Summary: This study describes the engineering of yeast strains to de novo produce bisbenzylisoquinoline alkaloids, and achieves high yields through optimization. By replacing cytochrome P450 in the reaction, the product profile can be altered. Furthermore, the inclusion of additional biosynthetic enzymes allows for the production of more derivatives.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Physical
Libo Zhang, Shiqing Zhang, Lijing Liao, Huanying Tang, Wenli Wang, Fucheng Yin, Liangliang Han, Kejin Zhu, Yushi Liu, Dingqiao Xu, Xiaobing Wang, Minjian Qin, Yibei Xiao, Xiang Sheng, Yucheng Zhao
Summary: Benzylisoquinoline alkaloids (BIAs) are important plant metabolites that offer pharmacological benefits. This study identified non-selective NCS homologues in lotus and revealed the biosynthesis pathway of (R)-BIAs.
Article
Biochemistry & Molecular Biology
Jan Stourac, Juraj Dubrava, Milos Musil, Jana Horackova, Jiri Damborsky, Stanislav Mazurenko, David Bednar
Summary: A majority of natural proteins have evolved to function in mild conditions inside organisms, causing challenges in their stability under extreme conditions. Predictors for stabilizing mutations are often used in biotechnological applications, with their accuracy relying on the quality and quantity of data used for training and testing. FireProt(DB) is a new database of experimental thermostability data for single-point mutants designed to address this issue.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Mingming Lu, Yadong Zhang, Fengchun Yang, Jialin Mai, Qianwen Gao, Xiaowei Xu, Hongyu Kang, Li Hou, Yunfei Shang, Qiheng Qain, Jie Liu, Meiye Jiang, Hao Zhang, Congfan Bu, Jinyue Wang, Zhewen Zhang, Zaichao Zhang, Jingyao Zeng, Jiao Li, Jingfa Xiao
Summary: Transcriptome-wide association studies have led to a better understanding of genetic variants in regulating diseases and traits. However, there is a lack of databases curating public TWAS information. To fill this gap, TWAS Atlas is introduced as an integrated knowledgebase with 401,266 gene-trait associations from 200 publications, providing a user-friendly web interface for browsing, searching, and downloading relevant information.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Qingqing Huang, Zhengtang Tan, Yanjing Li, Wenzhu Wang, Mei Lang, Changying Li, Zhiyun Guo
Summary: TFcancer is a database that collects experimentally supported associations between transcription factors and 33 TCGA cancers, providing valuable information on TF expression, molecular alterations, regulatory relationships, biological processes, and signaling pathways in cancers. It is a useful resource for researchers seeking to understand the functions and molecular mechanisms of TFs involved in human cancers.
Review
Plant Sciences
Harsh Singh, Dharmendra Singh, Manoj M. Lekhak
Summary: Thalictrum plants are known for their important alkaloids with various pharmacological activities. They have multiple chemical components and have the potential for further exploration and utilization.
JOURNAL OF ETHNOPHARMACOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Yan Huang, Jing Wang, Yue Zhao, Huafeng Wang, Tianyuan Liu, Yuhe Li, Tianyu Cui, Weiyi Li, Yige Feng, Jiaxin Luo, Jiaqi Gong, Lin Ning, Yong Zhang, Dong Wang, Yang Zhang
Summary: The article discusses the study of RNA with both protein-coding and noncoding functions, introduces the cncRNAdb database developed to provide a resource for manipulation, browsing, and analysis of cncRNAs. The database contains over 2000 RNAs from various species.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Plant Sciences
Weijia Cheng, Yan Yao, Qiuxia Wang, Xiaosa Chang, Zhuolin Shi, Xueting Fang, Fangfang Chen, Shixin Chen, Yonghong Zhang, Fan Zhang, Dongqing Zhu, Zixin Deng, Li Lu
Summary: In this study, novel BIA methyltransferases (MTs) were identified and characterized from Liriodendron chinense. Mutagenesis experiments revealed that a single-residue alteration is sufficient to change the substrate selectivity of these enzymes. This research sheds light on the molecular origin of BIAs during angiosperm evolution and provides valuable insights for the biosynthetic production of BIAs.
Article
Biochemistry & Molecular Biology
Jifeng Zhang, Shoubao Yan, Ruoyu Li, Gangyuan Wang, Siyong Kang, Ying Wang, Wenmin Hou, Chenrun Wang, Weidong Tian
Summary: CRMarker is a manually curated comprehensive repository of cancer RNA markers, containing 5489 known cancer RNA markers and over 18,000 potential cancer RNA markers. The database provides comprehensive search results, facilitating inquiries and retrievals for cancer researchers and clinicians.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Review
Pharmacology & Pharmacy
Sadhana Tripathi, Neelam Sharma, Leimarembi Devi Naorem, Gajendra P. S. Raghava
Summary: Over the years, numerous vaccines have been developed against viral infections, but a comprehensive database providing detailed information on viral vaccines has been lacking. In this review, we introduce our freely accessible database ViralVacDB, which includes details of viral vaccines, their types, routes of administration, and approving agencies. This repository systematically covers additional information on 422 viral vaccines, including 145 approved vaccines and 277 in clinical trials. We believe that this database will greatly benefit researchers and professionals in pharmaceuticals and immuno-informatics.
DRUG DISCOVERY TODAY
(2023)
Review
Biochemistry & Molecular Biology
Jose Ignacio Laines-Hidalgo, Jose Armando Munoz-Sanchez, Lloyd Loza-Muller, Felipe Vazquez-Flota
Summary: Benzophenanthridines are important benzylisoquinolic alkaloids that provide chemical protection in various plants. Despite their toxic nature, they have been used in traditional medicine as antimicrobial and antiprotozoal agents. The study of their biosynthetic pathways has led to a better understanding and potential exploitation of these compounds using modern biotechnological approaches.
