Biology subjects

Shimizu, K.

Publications and source records attributed to Shimizu, K..

3 recordsLinked to original sources

bioRxiv2018

Structural basis of HEAT-kleisin interactions in the human condensin I subcomplex

ABSTRUCTCondensin I is a multi-protein complex that plays an essential role in mitotic chromosome assembly and segregation in eukaryotes. It is composed of five subunits: two SMC (SMC2 and SMC4), a kleisin (CAP-H) and two HEAT-repeat (CAP-D2 and -G) subunits. Although it has been shown that balancing acts of the two HEAT-repeat subunits enable this complex to support dynamic assembly of chromosomal axes in vertebrate cells, its underlying mechanisms remain poorly understood. Here, we report the crystal structure of a human condensin I subcomplex comprising hCAP-G and hCAP-H. hCAP-H binds to the concave surfaces of a harp-shaped HEAT repeat domain of hCAP-G. A physical interaction between hCAP-G and hCAP-H is indeed essential for mitotic chromosome assembly recapitulated in Xenopus egg cell-free extracts. Furthermore, this study reveals that the human CAP-G-H subcomplex has the ability to interact with not only a double-stranded DNA, but also a single-stranded DNA, implicating potential, functional divergence of the vertebrate condensin I complex in mitotic chromosome assembly.

cell biology↗

bioRxiv2018

CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA-sequencing

Recent technical improvements in single-cell RNA sequencing (scRNA-seq) have enabled massively parallel profiling of transcriptomes, thereby promoting large-scale studies encompassing a wide range of cell types of multicellular organisms. With this background, we propose CellFishing.jl, a new method for searching atlas-scale datasets for similar cells and detecting noteworthy genes of query cells with high accuracy and throughput. Using multiple scRNA-seq datasets, we validate that our method demonstrates comparable accuracy to and is markedly faster than the state-of-the-art software. Moreover, CellFishing.jl is scalable to more than one million cells, and the throughput of the search is approximately 1,600 cells per second.

bioinformatics↗

bioRxiv2016

Secure Wavelet Matrix: Alphabet-Friendly Privacy-Preserving String Search

MotivationPrivacy-preserving substring matching is an important task for sensitive biological/biomedical sequence database searches. It enables a user to obtain only a substring match while his/her query is concealed to a server. The previous approach for this task is based on a linear-time algorithm in terms of alphabet size |{Sigma}|. Therefore, a more efficient method is needed to deal with strings with large alphabet size such as a protein sequence, time-series data, and a clinical document.\n\nResultsWe present a novel algorithm that can search a string in logarithmic time of |{Sigma}|. In our algorithm, named secure wavelet matrix (sWM), we use an additively homomorphic encryption to build an efficient data structure called a wavelet matrix. In an experiment using a simulated string of length 10,000 whose alphabet size ranges from 4 to 1024, the run time of the sWM was an order of magnitude faster than that of the previous method. We also tested the sWM on all sequences of one protein family in Pfam (9,826 residues in total) and clinical texts written in a natural language (77,712 letters in total). By using a laptop computer for the user and a desktop PC for the server, we found that its run time was {approx} 2.5 s (user) and {approx} 6.7 s (server) for the protein sequences and {approx} 10 s (user) and {approx} 60 s (server) for the clinical texts.\n\nAvailabilityhttps://github.com/cBioLab/sWM

bioinformatics↗