Biology subjects

Asami, Y.

Publications and source records attributed to Asami, Y..

3 recordsLinked to original sources

bioRxiv2026

Improved adenine-HPLC method for quantifying yeast based on cellular DNA content

Accurate quantification of fungi is important for a myriad of applications but remains challenging. Previously, we demonstrated that an approach called the adenine-HPLC method can quantify bacteria, including those with aggregating properties that are difficult to quantify using conventional methods, by measuring cellular adenine derived from DNA and converting the adenine amount to genome copy number, without being influenced by cell morphology. However, in this study, when this adenine-HPLC method was applied to the quantification of budding yeast as a model fungus, accurate measurement proved impossible. This limitation was attributed to adenine release from other adenine-containing biomolecules, such as RNA and ATP, and we therefore developed a method that suppresses adenine release from these molecules. This method involves reducing the temperature of the acid treatment and prewashing the cells before acid treatment. In addition, we incorporated a process that corrects for the naturally occurring free adenine level as background during total adenine measurement. The improved adenine-HPLC method based on these modifications enables accurate quantification of budding yeast using genomic DNA content in whole cells as the quantification unit.

microbiology↗

bioRxiv2024

Highly Sequence-specific, Timing-controllable m6A Demethylation by Modulating RNA-binding Affinity of m6A Erasers

In recent years, significant progress has been made in developing tools that consist of programmable RNA binding proteins and m6A-erasers to selectively demethylate m6A at specific sites. Especially, timing-controllable demethylation tools using stimulus-inducible dimerization show promise in understanding the impact of individual m6A modifications on dynamic physiological processes. However, a critical issue with these technologies is the possible off-target effects, wherein wild-type m6A-erasers constituting the tools may decrease methylation levels at sites other than the intended target m6A. In this study, we addressed this issue by reducing the intrinsic RNA-binding ability of m6A-erasers to prevent off-target effects and by fusing with PUF RNA-binding protein to provide recognition ability of arbitrary RNA sequences. Taking advantage of the reduced RNA-binding ability of the m6A-erasers themselves, we employed a rapamycin-based switching system in the linker connecting the PUF and m6A-eraser domains. The resulting m6A-erasers exhibited superior precision in demethylating targeted sites while minimizing off-target effects, presenting a novel approach for precise temporal control over m6A modification dynamics.

biochemistry↗

bioRxiv2017

Evaluation of variability in human protein X-ray structures

Systematic analysis of statistical and dynamical properties of proteins is critical to understanding cellular events. Extraction of biologically relevant information from a set of high-resolution structures is important because it can provide mechanistic details behind the functional properties of protein families, enabling rational comparison between families. Most of the current structure comparisons are pairwise-based, which hampers the global analysis of increasing contents in the Protein Data Bank. Additionally, pairing of protein structures introduces uncertainty with respect to reproducibility because it frequently accompanies other settings for superimposition. This study introduces intramolecular distance scoring, for the analysis of human proteins, for each of which at least several high-resolution are available. We show that the results are comprehensively used to overview advances at the atomic level exploration of each protein and protein family. This method, and the interpretation based on model calculations, provide new criteria for understanding specific and non-specific structure variation in a protein, enabling global comparison of the dynamics among a vast variety of proteins from different species.

biophysics↗