Identification of kinases and regulatory proteins required for cell migration using a transfected cell-microarray system.

Background: Cell migration plays a major role in a variety of normal biological processes, and a detailed understanding of the associated mechanisms should lead to advances in the medical sciences in areas such as cancer therapy. Previously, we developed a simple chip, based on transfected-cell microarray (TCM) technology, for the identification of genes related to cell migration. In the present study, we used the TCM chip for high-throughput screening (HTS) of a kinome siRNA library to identify genes involved in the motility of highly invasive NBT-L2b cells.

Development of a microfabricated device for low-voltage electropermeabilization of adherent cells.

A microfabricated device for low-voltage electropermeabilization of adherent cells has been developed. The device, which is fabricated on a cover glass using mainly transparent materials, allows optical observation of cells through it. This device consists of an array of 6-μm circular electrodes connected via a transparent and conductive layer made of ITO (indium tin oxide) to give pulsed voltages for electropermeabilization.

Motility behavior of rpoS-deficient Escherichia coli analyzed by individual cell tracking.

Motility is one of the most extensively studied cellular events conducted by bacteria, including Escherichia coli. A motility agar plate assay showed that deletion of the rpoS gene enhanced the apparent motility of the E. coli BW25113 strain, which inherently had negligible motility compared to wild-type E.

Evaluation method for gene transfection by using the period of onset of gene expression and cell division.

Using single-cells time-lapse analysis, we investigated the mechanism of gene expression using nine transfection reagents. Although onset of gene expression occurred after cell division by all reagents, 91.6% periods, which depended on onset and cell division, had statistical significance.

Transfection microarrays for high-throughput phenotypic screening of genes involved in cell migration.

Cell migration is important in several biological phenomena, such as cancer metastasis. Therefore, the identification of genes involved in cell migration might facilitate the discovery of antimetastatic drugs. However, screening of genes by the current methods can be complicated by factors related to cell stimulation, for example, abolition of contact inhibition and the release inflammatory cytokines from wounded cells during examinations of wound healing in vitro.

Onset timing of transient gene expression depends on cell division.

By using the time lapse of both phase-contrast and fluorescent images, we examined the morphology of cells and the dynamics of gene expression (EGFP). We applied k-means clustering to the time course data of fluorescent intensity of EGFP and successfully found four subpopulations. Discriminating the appropriate clusters and investigating the details of them, we found that almost all cells express the transfected gene after cell division and also found there is a strong correlation between onset timing and cell division.

On-chip screening method for cell migration genes based on a transfection microarray.

Cell migration plays a major role in a variety of biological processes and a detailed understanding of associated mechanisms should lead to advances in the medical sciences, for example, in drug discovery for cancer therapy. However, the traditional methods used for analysis of cell migration cannot easily be scaled up for high-throughput screening. In this study, we have attempted to develop a novel simple method for high-throughput phenotypic screening for the identification of genes that are required for cell migration.

A system for analyzing the event timing profile of single cells by using a model of neurite maturation in PC12D cells.

Nerve growth factor (NGF)-induced neurite maturation in PC12D cells involves neuritogenesis and neurite outgrowth. Actions of compounds affecting the neurite maturation are sometimes invisible behind the individually variable events in nature even in the clonal population. In this study, we designed a time-lapse imaging system to determine the timing of each event in individual PC12D cells.

Modified fuzzy gap statistic for estimating preferable number of clusters in fuzzy k-means clustering.

In clustering methods, the estimation of the optimal number of clusters is significant for subsequent analysis. Without detailed biological information on the genes involved, the evaluation of the number of clusters becomes difficult, and we have to rely on an internal measure that is based on the distribution of the data of the clustering result. The Gap statistic has been proposed as a superior method for estimating the number of clusters in crisp clustering.

Novel technique for preprocessing high dimensional time-course data from DNA microarray: mathematical model-based clustering.

Motivation: Classifying genes into clusters depending on their expression profiles is one of the most important analysis techniques for microarray data. Because temporal gene expression profiles are indicative of the dynamic functional properties of genes, the application of clustering analysis to time-course data allows the more precise division of genes into functional classes. Conventional clustering methods treat the sampling data at each time point as data obtained under different experimental conditions without considering the continuity of time-course data between time periods t and t+1.

A preprocessing method for inferring genetic interaction from gene expression data using Boolean algorithm.

Unknown genetic regulation mechanisms are expected to be discovered by information technology using large amount of biological data especially for gene expression data. In this study, we propose a novel inferring method for genetic interactions that combines our original preprocessing method and the Boolean algorithm. First, the performance of our method was evaluated using artificial data.