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Plasmids

Plasmids

Plasmids are extrachromosomal DNA molecules found in bacteria, archaea, and some eukaryotic microbes like yeast. These small, circular DNA structures typically contain fewer than 30 genes, although some may exist linearly. Plasmids vary in their number within a cell, known as copy number. Single-copy plasmids are present in one copy per cell and multi-copy plasmids are present in multiple copies, reaching over 100 copies per cell.Plasmids usually replicate independently of the chromosomal DNA...

Modern Molecular Taxonomy

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...

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Updated: May 6, 2026

Quantification of Plasmid-Mediated Antibiotic Resistance in an Experimental Evolution Approach

Quantification of Plasmid-Mediated Antibiotic Resistance in an Experimental Evolution Approach

Published on: December 14, 2019

MOSTPLAS: a self-correction multi-label learning model for plasmid host range prediction.

Wei Zou¹, Yongxin Ji¹, Jiaojiao Guan¹

¹Department of Electrical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, China.

Bioinformatics (Oxford, England)

|February 17, 2025

Summary

This summary is machine-generated.

A new self-correction model, MOSTPLAS, accurately predicts plasmid host ranges, even with incomplete data. This advances understanding of bacterial evolution and horizontal gene transfer.

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Last Updated: May 6, 2026

Quantification of Plasmid-Mediated Antibiotic Resistance in an Experimental Evolution Approach

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Published on: December 14, 2019

Detection of Horizontal Gene Transfer Mediated by Natural Conjugative Plasmids in E. coli

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Published on: March 24, 2023

Plasmid Stability Analysis with Open-Source Droplet Microfluidics

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Published on: December 27, 2024

Area of Science:

Microbiology
Bioinformatics
Computational Biology

Background:

Plasmids are key drivers of bacterial evolution via horizontal gene transfer, conferring traits like antibiotic resistance.
Broad-host-range plasmids can persist across multiple organisms, making their host range identification crucial for understanding bacterial adaptation.
Current limitations in comprehensive plasmid host range data hinder the development of accurate predictive models.

Purpose of the Study:

To develop a robust computational model for predicting the host range of broad-host-range plasmids.
To address the challenge of incomplete and missing label data in plasmid host range datasets.
To improve the accuracy and comprehensiveness of plasmid host range predictions.

Main Methods:

Proposed a novel self-correction multi-label learning model named MOSTPLAS.
Implemented a pseudo-label learning algorithm and a self-correction asymmetric loss function to handle missing labels.
Validated the model using diverse datasets including NCBI RefSeq, PLSDB 2025, and experimentally determined host labels.

Main Results:

MOSTPLAS demonstrated superior performance in identifying a greater number of host labels compared to existing tools.
The model maintained high precision in its predictions, indicating reliability.
Experimental results confirmed the effectiveness of the self-correction mechanism in handling incomplete data.

Conclusions:

MOSTPLAS offers a significant advancement in predicting plasmid host ranges, particularly for broad-host-range plasmids.
The model's ability to handle missing labels overcomes a critical bottleneck in existing methods.
This work provides a valuable tool for researchers studying plasmid biology and bacterial evolution.