National Institute of Genetics

Mishima, Japan

National Institute of Genetics

Mishima, Japan
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Takahashi A.,National Institute of Genetics | Miczek K.A.,Tufts University
Current Topics in Behavioral Neurosciences | Year: 2015

At the end of this chapter, we discuss how genes can be identified that underlie individual differences in aggression, using the so-called forward genetics approach. © Springer-Verlag Berlin Heidelberg 2013

Kodama Y.,National Institute of Genetics | Shumway M.,U.S. National Center for Biotechnology Information | Leinonen R.,European Bioinformatics Institute
Nucleic Acids Research | Year: 2012

New generation sequencing platforms are producing data with significantly higher throughput and lower cost. A portion of this capacity is devoted to individual and community scientific projects. As these projects reach publication, raw sequencing datasets are submitted into the primary next-generation sequence data archive, the Sequence Read Archive (SRA). Archiving experimental data is the key to the progress of reproducible science. The SRA was established as a public repository for next-generation sequence data as a part of the International Nucleotide Sequence Database Collaboration (INSDC). INSDC is composed of the National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EBI) and the DNA Data Bank of Japan (DDBJ). The SRA is accessible at from NCBI, at from EBI and at from DDBJ. In this article, we present the content and structure of the SRA and report on updated metadata structures, submission file formats and supported sequencing platforms. We also briefly outline our various responses to the challenge of explosive data growth. © The Author(s) 2011.

Ohta T.,National Institute of Genetics
Genome Biology and Evolution | Year: 2011

The nearly neutral theory emphasizes the interaction of drift and weak selection in evolution. With progress of genome biology, the applicability of the nearly neutral theory has expanded. The genome-wide analyses of synonymous and nonsynonymous substitutions at protein-coding regions show prevalence of very weak selection. Many patterns of evolution of gene regulation are also in agreement with the nearly neutral prediction. Our consideration on near-neutrality expands in relation to the progress on molecular understanding of robustness and epigenetics. Both are bridges to link genotypes with phenotypes and important for understanding how weak selection and drift interact in the evolution of complex systems. © The Author(s) 2010.

Araki H.,National Institute of Genetics
Current Opinion in Cell Biology | Year: 2010

Cyclin-dependent kinase (CDK) is essential for the initiation of chromosomal DNA replication. CDK phosphorylates two yeast replication proteins, Sld2 and Sld3, both of which bind to another replication protein, Dpb11 when phosphorylated. These interactions are essential and are the minimal requirements for CDK activation of chromosomal DNA replication. This review discusses how these phosphorylation-dependent interactions initiate DNA replication through the formation of the pre-loading complex (pre-LC) and its interaction with phosphorylated Sld3 on replication origins. These steps are further regulated by multisite phosphorylation of Sld2. Sld3, on the other hand, must be turned over to reassociate with origins. Pol e{open} functions as a component of the pre-LC as well as a replicative DNA polymerase at replication forks. © 2010 Elsevier Ltd.

Goshima G.,Nagoya University | Kimura A.,National Institute of Genetics
Current Opinion in Cell Biology | Year: 2010

The structure, dynamics, and mechanics of mitotic and meiotic spindles have been progressively elucidated through the advancements in microscopic technology, identification of the genes involved, and construction of theoretical frameworks. Here, we review recent works that have utilized quantitative image analysis to advance our understanding of the complex spindle structure of animal cells. In particular, we discuss how microtubules (MTs) are nucleated and distributed inside the spindle. Accumulating evidence supports the presence of MT-dependent MT generation within the spindle. This mechanism would produce dense arrays of intraspindle MTs with various lengths, which may contribute to efficient spindle assembly and stabilize the metaphase spindle. RNA interference (RNAi) screens with quantitative image analysis led to the identification of the augmin complex that plays a key role in this MT generation process. © 2009 Elsevier Ltd. All rights reserved.

Shimizu H.,National Institute of Genetics
International Journal of Developmental Biology | Year: 2012

Since the pioneering work of Ethel Browne (1909) who demonstrated for the first time the concept of organizer activity, i.e. the potency of an apical Hydra tissue to induce a secondary axis when transplanted onto a host, Hydra flourished as a fruitful model system for developmental studies. Over the next 60 years this efficient transplantation approach identified graded biological activities along the body column of Hydra named Head Activation and Head Inhibition. These properties inspired theoretical modelers including Lewis Wolpert, Alfred Gierer and Hans Meinhardt to propose models for morphogenesis, respectively the positional information (1969) and reaction-diffusion (1972) models. In 1973, Tsutomu Sugiyama and Toshitaka Fujisawa initiated in Mishima a unique project to analyze the properties of Hydra strains with distinct morphological and developmental characters. To this end, they collected in several areas of Japan multiple Hydra strains that they subsequently characterized and crossed. They also established a lateral transplantation strategy that was much more powerful than the previous ones, as it combined quantitative measurements with cellular analyses thanks to the chimera procedures developed by Campbell and colleagues. Indeed this approach provided a paradigm to quantify in any morphological phenotype the Head Activation and Head Inhibition levels along the body column. In this article, I review the various strains identified by Sugiyama and colleagues, the principles and the main results deduced from the quantitative lateral transplantation strategy. In addition, I briefly discuss the relevance of this approach in the era of molecular biology. © UBC Press.

Yoshiba S.,Osaka University | Yoshiba S.,National Institute of Genetics | Hamada H.,Osaka University
Trends in Genetics | Year: 2014

The emergence of left-right (L-R) asymmetry during embryogenesis is a classic problem in developmental biology. It is only since the 1990s, however, that substantial insight into this problem has been achieved by molecular and genetic approaches. Various genes required for L-R asymmetric morphogenesis in vertebrates have now been identified, and many of these genes are required for the formation and motility of cilia. Breaking of L-R symmetry in the mouse embryo occurs in the ventral node, where two types of cilia are present. Whereas centrally located motile cilia generate a leftward fluid flow, peripherally located immotile cilia sense a flow-dependent signal, which is either chemical or mechanical in nature. Although Ca2+ signaling is implicated in flow sensing, the precise mechanism remains unknown. Here we summarize current knowledge of L-R symmetry breaking in vertebrates (focusing on the mouse), with a special emphasis on the roles of cilia, fluid flow, and Ca2+ signaling. © 2013 Elsevier Ltd.

Sawa H.,National Institute of Genetics
Current Topics in Developmental Biology | Year: 2012

During development of Caenorhabditis elegans, most somatic cells divide asymmetrically to produce daughter cells with distinct fates. A Wnt signaling pathway called Wnt/β-catenin asymmetry pathway controls both polarity of mother cells and distinct fates of daughter cells. Unlike the PCP pathway that regulates cell polarity in other organisms, this Wnt pathway in C. elegans requires β-catenin. However, similar to the PCP pathway, signaling components including Dishevelled proteins are asymmetrically localized to the cell cortex. I will review current knowledge about the mechanism of this regulation and how the orientation of cell polarity is controlled by Wnt proteins. © 2012 Elsevier Inc.

Sugioka K.,National Institute of Genetics | Sawa H.,National Institute of Genetics
Current Opinion in Cell Biology | Year: 2012

Although microtubules are known to be essential for chromosome segregation during cell division, they also play important roles in the regulation and function of cell polarity. Cell polarization is fundamental to appropriate tissue patterning and the regulation of cellular diversity during animal development. In polarized cells, microtubules are often organized asymmetrically along the polarity axis. Recent studies show that such asymmetry in microtubule organization is important to connect a cell's polarization with its polarized functions. In some cases, asymmetrically organized microtubule arrays themselves induce cell polarity. Here we present an overview of the mechanisms and functions of asymmetric microtubule organization and discuss the possible role of microtubule asymmetry in the symmetry-breaking that leads to cell polarization. © 2012 Elsevier Ltd.

Kanemaki M.T.,National Institute of Genetics
Pflugers Archiv European Journal of Physiology | Year: 2013

It is useful to artificially control the expression levels of a protein of interest (POI), not only for its characterization in vivo, but also for the modulation of biological pathways. Overexpression of a POI is relatively easy because it is possible to drive its expression from a transgene encoding the POI under the control of a strong promoter. However, it is more challenging to reduce or deplete the expression of a POI. A protein domain called "degron", which induces rapid proteolysis by the proteasome, can be used for this purpose. Degron-based technologies for the conditional depletion of POI - degron fusion proteins have been developed by exploiting various pathways leading to proteasomal degradation. Compared with other depletion technologies that control the expression levels of POIs at the DNA or mRNA levels, these protein-depletion approaches are advantageous in terms of specificity, reversibility, and the time required for depletion. Current conditional degron-based technologies are described and discussed. © 2012 Springer-Verlag Berlin Heidelberg.

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