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Biology subjects

Li, D. R.

Publications and source records attributed to Li, D. R..

3 recordsLinked to original sources

Synaptic adhesion molecule signaling is activated and organized by tyrosine phosphorylation-induced biomolecular condensate formation

The precise formation of synapses ensures the proper wiring and function of nervous systems. Specific synapse formation is controlled by synaptic adhesion molecules, which link pre- and post-synaptic cells. Despite this central role, details of how adhesion molecules organize and signal intracellularly to build core synaptic structures are limited. Here, we identify multiple tyrosine phosphorylation sites on the cytoplasmic tail of the C. elegans SYG-1 synaptic adhesion molecule that are critical to initiate presynapse formation. We determine that SRC-1 and SRC-2 tyrosine kinases are redundantly responsible for SYG-1 phosphorylation and are consequently critical for presynapse assembly. The phosphorylated population of SYG-1 localizes in clusters within a larger SYG-1 pool and these clusters mark sites of presynaptic active zone assembly. Reconstitution of SYG-1 clusters in vitro with SH2-domain adapters and WSP-1 reveals a dynamic biomolecular condensate-forming system. Blocking phosphotyrosine adapters and condensate formation in vivo results in the loss of SYG-1 clusters, defective presynapse formation, and compromised neurotransmission. We conclude that phosphorylation of a subpopulation of synaptic adhesion molecules activates and organizes them into condensate-based clusters to initiate presynapse formation.

neuroscience↗

MicroWorldOmics:A "One step for All" desktop application for comprehensive analysis in microbiome and virome and exploring "Dark Matter" from MicroWorld

A large amount of high-throughput sequencing data generated in ecology, medicine, and pharmacy has increasingly raised the complexity of data analysis and interpretation. However, the microbiome and virome field still lacks a convenient and programming-free desktop application for the comprehensive analysis in microbiome and virome data, particularly in virome analysis and Dark Matter exploration. Therefore, a plugin development mode desktop service, MicroWorldOmics, is proposed with a convenient and one-stop pipeline for life sciences and biomedical fields. Plugin development allows users to analyze data in parallel and interactively, while these tasks usually require advanced bioinformatician to achieve. MicroWorldOmics is a software widely used in microbiome and virome, containing 90 sub-applications, including four main functions: epidemiological analysis, metagenomic/amplicons and virome comprehensive analysis, and exploring Dark matter. More than 80 Python modules and 600 R packages are invoked in all aspects of bioinformatics analysis, statistical analysis, deep learning, and visualization. At the same time, the software supports multiple input and output results, such as GFF3, FASTA, CSV, PNG, JPG, JSON, and TXT, etc. Besides, to improve the efficiency for users, MicroWorldOmics supports being deployed in three mainstream systems: Windows, Linux, and Mac and also sets the demo/example data for users to test the benchmark easily. In summary, the development of MicroWorldOmics greatly facilitates the process of analyzing microbiome and virome data for researchers who have no programming foundation and are devoted to life science and biomedicine data analysis.

genomics↗

ESKtides: a comprehensive database and mining method for ESKAPE-derived peptides

Under the concept of one health, Super-drug resistant bacteria are getting more and more attention from scientists, in particular, ESKAPE bacteria directly killed more than 1,270,000 people in 2019. Recent studies have proposed that phage PGHs(peptidoglycan hydrolases) and antimicrobial peptides can be the new antibacterial agents against multi-drug resistant bacteria. However, Methods for mining antimicrobial peptides based on phages or phages PGHs are in need to develop. Here, using ESKAPE strains and ESKAPE phages in total of 6,809 samples from National Center for Biotechnology Information (NCBI), PhagesDB, Microbe Versus Phage (MVP) and Virus-Host Database, we systematically identified PGHs across ESKAPE strains prophages and phages, mined peptides and scored peptides based on PGHs. As a result, a total of 1,000 high antibacterial activity peptides and 1,200 medium antibacterial activity peptides were identified. In order to reduce the impact of different methods on comments, we used a unified process to comment ESKAPE strains and phages. In addition, we designed an online tool to predict the peptides antibacterial activity. Calculations of peptides phylogeny, peptides physicochemical property and peptides secondary structure are also included into our online tools. Finally, we developed ESKtides, a user-friendly and intuitive database (http://www.phageonehealth.cn:9000/ESKtides) for data browsing, searching, and downloading. ESKtides will significantly provide a rich peptide library based on ESKAPE strains and phages.

bioinformatics↗