Efficient, robust, and versatile fluctuation data analysis using MLE MUtation Rate calculator (mlemur)

Area of Science:

• Microbiology
• Genetics
• Computational Biology

Background:

• The fluctuation assay is crucial for analyzing microbial mutagenesis.
• Existing tools for mutation rate estimation may lack accuracy under non-standard conditions.
• The Luria-Delbrück distribution is commonly used but has limitations in realistic biological contexts.

Purpose of the Study:

• To extend the Luria-Delbrück protocol to account for phenotypic lag and cellular death.
• To develop a user-friendly tool (mlemur) for accurate mutation rate estimation.
• To address limitations of current methods in complex experimental settings.

Main Methods:

• Developed extensions to the Luria-Delbrück protocol.
• Created the MLE MUtation Rate calculator (mlemur) with a graphical interface.
• Incorporated factors like phenotypic lag, cellular death, partial plating, and inoculum size.

Main Results:

• mlemur provides accurate estimates for mutation rates, P values, and confidence intervals.
• The tool allows simultaneous consideration of multiple non-standard conditions.
• Accuracy was validated against historical and simulated fluctuation experiments.

Conclusions:

• mlemur is the first tool to offer a user-friendly interface for complex fluctuation assay modeling.
• The tool enhances the accuracy of mutation rate estimation in realistic biological scenarios.
• This work highlights the limitations of the Lea-Coulson formulation and offers a more versatile alternative.