SHARPIN is a component of the NF-κB-activating linear ubiquitin chain assembly complex

Cpdm (chronic proliferative dermatitis) mice develop chronic dermatitis and an immunodeficiency with increased serum IgM, symptoms that resemble those of patients with X-linked hyper-IgM syndrome and hypohydrotic ectodermal dysplasia (XHM-ED), which is caused by mutations in NEMO (NF-κB essential modulator; also known as IKBKG). Spontaneous null mutations in the Sharpin (SHANK-associated RH domain interacting protein in postsynaptic density) gene are responsible for the cpdm phenotype in mice. SHARPIN shows significant similarity to HOIL-1L (also known as RBCK1), a component of linear ubiquitin chain assembly complex (LUBAC), which induces NF-κB activation through conjugation of linear polyubiquitin chains to NEMO. Here, we identify SHARPIN as an additional component of LUBAC. SHARPIN-containing complexes can linearly ubiquitinate NEMO and activated NF-κB. Thus, we re-define LUBAC as a complex containing SHARPIN, HOIL-1L, and HOIP (also known as RNF31). Deletion of SHARPIN drastically reduced the amount of LUBAC, which resulted in attenuated TNF-α- and CD40-mediated activation of NF-κB in mouse embryonic fibroblasts (MEFs) or B cells from cpdm mice. Considering the pleomorphic phenotype of cpdm mice, these results confirm the predicted role of LUBAC-mediated linear polyubiquitination in NF-κB activation induced by various stimuli, and strongly suggest the involvement of LUBAC-induced NF-κB activation in various disorders.     

Connecting informal networks to management of tacit knowledge

The relationship between tacit knowledge and informal networks has not been fully explored.Tacit knowledge cannot be well managed directly,because it is deeply embedded in individual actions and experiences.This study proposes an approach to managing informal networks as a new middle way to facilitate the sharing and transferring of tacit knowledge,owing to the fact that tacit knowledge is mostly shared and transferred through informal networks.To support the idea of the approach,an empirical case study of applying the approach to management of a large scientific project is also included.Our findings suggest that informal networks play essential roles for management of tacit knowledge,and thus good management of informal networks can lead to efficient sharing and transferring of tacit knowledge.     

Knowledge-scientific evaluation of community service systems

This paper proposes a knowledge-scientific approach to evaluation of community service systems from the viewpoints of knowledge creation, consciousness reform, and value co-creation. A concrete example of the community service system treated here is an education program for old men to find their reason for living after the retirement. After introducing this program and the traditional evaluation methods for such a program, the paper emphasizes the necessity of developing new evaluation methods for such a community service system based on knowledge science. The paper proposes a new evaluation framework and reports an actual evaluation result using the interview data from participants in that program.     

The genome sequence and structure of rice chromosome 1

The rice species Oryza sativa is considered to be a model plant because of its small genome size, extensive genetic map, relative ease of transformation and synteny with other cereal crops. Here we report the essentially complete sequence of chromosome 1, the longest chromosome in the rice genome. We summarize characteristics of the chromosome structure and the biological insight gained from the sequence. The analysis of 43.3 megabases (Mb) of non-overlapping sequence reveals 6,756 protein coding genes, of which 3,161 show homology to proteins of Arabidopsis thaliana, another model plant. About 30% (2,073) of the genes have been functionally categorized. Rice chromosome 1 is (G + C)-rich, especially in its coding regions, and is characterized by several gene families that are dispersed or arranged in tandem repeats. Comparison with a draft sequence indicates the importance of a high-quality finished sequence.     

A CLUSTERING ALGORITHM FOR MIXED NUMERIC AND CATEGORICAL DATA

Most of the earlier work on clustering mainly focused on numeric data whose inherent geometric properties can be exploited to naturally define distance functions between data points. However, data mining applications frequently involve many datasets that also consists of mixed numeric and categorical attributes. In this paper we present a clustering algorithm which is based on the k-means algorithm. The algorithm clusters objects with numeric and categorical attributes in a way similar to k-means. The object similarity measure is derived from both numeric and categorical attributes. When applied to numeric data, the algorithm is identical to the k-means. The main result of this paper is to provide a method to update the “cluster centers“ of clustering objects described by mixed numeric and categorical attributes in the clustering process to minimise the clustering cost function. The clustering performance of the algorithm is demonstrated with the two well known data sets, namely credit approval and abalone databases.     

Nck adaptor proteins link nephrin to the actin cytoskeleton of kidney podocytes

The glomerular filtration barrier in the kidney is formed in part by a specialized intercellular junction known as the slit diaphragm, which connects adjacent actin-based foot processes of kidney epithelial cells (podocytes). Mutations affecting a number of slit diaphragm proteins, including nephrin (encoded by NPHS1), lead to renal disease owing to disruption of the filtration barrier and rearrangement of the actin cytoskeleton, although the molecular basis for this is unclear. Here we show that nephrin selectively binds the Src homology 2 (SH2)/SH3 domain-containing Nck adaptor proteins, which in turn control the podocyte cytoskeleton in vivo. The cytoplasmic tail of nephrin has multiple YDxV sites that form preferred binding motifs for the Nck SH2 domain once phosphorylated by Src-family kinases. We show that this Nck-nephrin interaction is required for nephrin-dependent actin reorganization. Selective deletion of Nck from podocytes of transgenic mice results in defects in the formation of foot processes and in congenital nephrotic syndrome. Together, these findings identify a physiological signalling pathway in which nephrin is linked through phosphotyrosine-based interactions to Nck adaptors, and thus to the underlying actin cytoskeleton in podocytes. Simple and widely expressed SH2/SH3 adaptor proteins can therefore direct the formation of a specialized cellular morphology in vivo.     

AGENT-BASED SIMULATION FOR KANSEI ENGINEERING： TESTING A FUZZY LINEAR QUANTIFICATION METHOD IN AN ARTIFICIAL WORLD

This paper argues that agent-based simulation can be used as a way for testing Kansei Engineering methods which deal with the human reaction from sensory to mental state, that is, sensitivity, sense, sensibility, feeling, esthetics, emotion affection and intuition. A new fuzzy linear quantification method is tested in an artificial world by agent-based modeling and simulations, and the performance of the fuzzy linear method is compared with that of a genetic algorithm. The simulations can expand people＇s imagination and enhance people＇s intuition that the new fuzzy linear quantification method is effective.     

Methane emissions from wetlands on the Qinghai-Tibet Plateau

The areal extent of cold freshwater wetlands on the Qinghai-Tibet Plateau (QTP) is estimated at 0.133 × 10⁶ km², suggesting a significant methane potential. Methane fluxes from wet alpine meadows, peatlands,Hippuris vulgaris mires and secondary marshes were 43.18, 12.96, −0.28 and 45.90 mg · m⁻² · d⁻¹, respectively based on the transect flux studies at the Huashixia Permafrost Station (HPS) from July to August 1996. Average CH₄ fluxes in the thaw season were extrapolated at 5.68 g · m⁻² according to the areal percentage of wetland areas in the Huashixia region. The CH₄ fluxes at four fixed sites, representative of similar ecosystems, ranged from −19.384–347.15 mg · m⁻² · d⁻¹, and the average CH₄ fluxes varied from 6.54 to 71.97 mg · m⁻² · d⁻¹ at each site during the observation period from April to September 1997. The CH₄ emissions at each site during the entire thaw season was estimated from 1.21 to 10.65 g · m⁻², displaying strong spatial variations. Seasonal variations of CH₄ fluxes also were observed at four sites: CH₄ outbursts occurred upon the spring thaw in May and June, CH₄ fluxes increased afterwards with rising soil temperatures. Episodic fluxes were observed in summer, which influenced the average CH₄ fluxes considerably. Annual CH₄ emissions from cold wetlands on the QTP were estimated at about 0.7–0.9 Tg based on the distribution of wetlands, representative CH₄ fluxes, and number of thaw days. The centers of CH₄ releasing were located in the sources of the Yangtze and Yellow rivers, and Zoigê Peatlands.     

Haploinsufficiency of NSD1 causes Sotos syndrome

We isolated NSD1 from the 5q35 breakpoint in an individual with Sotos syndrome harboring a chromosomal translocation. We identified 1 nonsense, 3 frameshift and 20 submicroscopic deletion mutations of NSD1 among 42 individuals with sporadic cases of Sotos syndrome. The results indicate that haploinsufficiency of NSD1 is the major cause of Sotos syndrome.     

The medaka draft genome and insights into vertebrate genome evolution

Teleosts comprise more than half of all vertebrate species and have adapted to a variety of marine and freshwater habitats. Their genome evolution and diversification are important subjects for the understanding of vertebrate evolution. Although draft genome sequences of two pufferfishes have been published, analysis of more fish genomes is desirable. Here we report a high-quality draft genome sequence of a small egg-laying freshwater teleost, medaka (Oryzias latipes). Medaka is native to East Asia and an excellent model system for a wide range of biology, including ecotoxicology, carcinogenesis, sex determination and developmental genetics. In the assembled medaka genome (700 megabases), which is less than half of the zebrafish genome, we predicted 20,141 genes, including approximately 2,900 new genes, using 5'-end serial analysis of gene expression tag information. We found single nucleotide polymorphisms (SNPs) at an average rate of 3.42% between the two inbred strains derived from two regional populations; this is the highest SNP rate seen in any vertebrate species. Analyses based on the dense SNP information show a strict genetic separation of 4 million years (Myr) between the two populations, and suggest that differential selective pressures acted on specific gene categories. Four-way comparisons with the human, pufferfish (Tetraodon), zebrafish and medaka genomes revealed that eight major interchromosomal rearrangements took place in a remarkably short period of approximately 50 Myr after the whole-genome duplication event in the teleost ancestor and afterwards, intriguingly, the medaka genome preserved its ancestral karyotype for more than 300 Myr.