The diagnosis and treatment of soft tissue sarcomas (STS) have been difficult. Of the diverse histological subtypes, undifferentiated pleomorphic sarcoma (UPS) is particularly difficult to diagnose accurately, and its classification per se is still controversial. Recent advances in genomic technologies provide an excellent way to address such problems. However, it is often difficult, if not impossible, to identify definitive disease-associated genes using genome-wide analysis alone, primarily because of multiple testing problems. In the present study, we analyzed microarray data from 88 STS patients using a combination method that used knowledge-based filtering and a simulation based on the integration of multiple statistics to reduce multiple testing problems. We identified 25 genes, including hypoxia-related genes (e.g., MIF, SCD1, P4HA1, ENO1, and STAT1) and cell cycle- and DNA repair-related genes (e.g., TACC3, PRDX1, PRKDC, and H2AFY). These genes showed significant differential expression among histological subtypes, including UPS, and showed associations with overall survival. STAT1 showed a strong association with overall survival in UPS patients (logrank p = 1.84×10−6 and adjusted p value 2.99×10−3 after the permutation test). According to the literature, the 25 genes selected are useful not only as markers of differential diagnosis but also as prognostic/predictive markers and/or therapeutic targets for STS. Our combination method can identify genes that are potential prognostic/predictive factors and/or therapeutic targets in STS and possibly in other cancers. These disease-associated genes deserve further preclinical and clinical validation.

The diagnosis and treatment of soft tissue sarcomas (STSs) has been particularly difficult, because STSs are a group of highly heterogeneous tumors in terms of histopathology, histological grade, and primary site. Recent advances in genome technologies have provided an excellent opportunity to determine the complete biological characteristics of neoplastic tissues, resulting in improved diagnosis, treatment selection, and investigation of therapeutic targets. We had previously developed a novel bioinformatics method for marker gene selection and applied this method to gene expression data from STS patients. This previous analysis revealed that the extracted gene combination of macrophage migration inhibitory factor (MIF) and stearoyl-CoA desaturase 1 (SCD1) is an effective diagnostic marker to discriminate between subtypes of STSs with highly different outcomes. In the present study, we hypothesize that the combination of MIF and SCD1 is also a prognostic marker for the overall outcome of STSs. To prove this hypothesis, we first analyzed microarray data from 88 STS patients and their outcomes. Our results show that the survival rates for MIF- and SCD1-positive groups were lower than those for negative groups, and the p values of the log-rank test are 0.0146 and 0.00606, respectively. In addition, survival rates are more significantly different (p = 0.000116) between groups that are double-positive and double-negative for MIF and SCD1. Furthermore, in vitro cell growth inhibition experiments by MIF and SCD1 inhibitors support the hypothesis. These results suggest that the gene set is useful as a prognostic marker associated with tumor progression.

Most bacterial cells in nature exhibit extremely low colony-forming activity, despite showing various signs of viability, impeding the isolation and utilization of many bacterial resources. However, the general causes responsible for this state of low colony formation are largely unknown. Because liquid cultivation typically yields more bacterial cell cultures than traditional solid cultivation, we hypothesized that colony formation requires one or more specific gene functions that are dispensable or less important for growth in liquid media. To verify our hypothesis and reveal the genetic background limiting colony formation among bacteria in nature, we isolated Escherichia coli mutants that had decreased frequencies of colony formation but could grow in liquid medium from a temperature-sensitive mutant collection. Mutations were identified in fabB, which is essential for the synthesis of long unsaturated fatty acids. We then constructed a fabB deletion mutant in a wild-type background. Detailed behavioural analysis of the mutant revealed that under fatty acid-limited conditions, colony formation on solid media was more sensitively and seriously impaired than growth in liquid media. Furthermore, growth under partial inhibition of fatty acid synthesis with cerulenin or triclosan brought about similar phenotypes, not only in E. coli but also in Bacillus subtilis and Corynebacterium glutamicum. These results indicate that fatty acids have a critical importance in colony formation and that depletion of fatty acids in the environment partly accounts for the low frequency of bacterial colony formation.

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Hand spun silk yarn made from floss silk is referred to as tsumugi yarn. It gives a unique appearance on the products, tsumugi, which are considered to be an important type of fabrics for their aesthetics.The essential factor of this visual effect is originated by the thickness variation of tsumugi yarn, however the detail of the variation is unknown. In this paper, as a fundamental study of tsumugi yarn, its width distribution is discussed. To model the width distribution, Polya-Eggenberger distribution is introduced. Moreover some modifications are applied for the distribution to describe the yarn situation.That is to say, it is impossible to be thinner than a level of thickness for the yarn to maintain a shape of a thread, on the other hand tsumugi yarn is not limited to contain some thicker parts in itself.Additionally, it is not avoidable to involve errors and fluctuations in the actual data. Hence the distribution is truncated and convoluted. By using an image scanner, the width of tsumugi yarn is measured. With the measured data, the parameters of the width distribution are estimated using the maximum likelihood method. The results shows that the width distribution of tsumugi yarn is asymmetric and well summarized by the distribution. Key wordstruncated distribution, tsumugi yarn, convolution, Polya-Eggenberuger distribution, maximum likelihood methodThe origin of tsumugi is utilization of inferior cocoons which cannot provide quality raw silk. By degumming and spreading the cocoons, floss silk is produced. Then the floss is processed by hand into tsumugi yarn which is very irregular in thickness due to the entanglement of the fibers in the floss silk.The yarn is raw material of tsumugi, a silk fabric with unique irregularity on its surface. Although it began as a secondary product, people became to find beauty in it. Nowadays, tsumugi is considered to be an important type of fabrics. Thus several techniques have been developed to introduce the effect into other kind of textiles. Although, it is easy to produce irregular and/or uneven yarns, it is difficult to generate intended effect on the produced textiles. In many cases, uneven yarns result in faults and/or defects on the products. It is surely that the characteristics of tsumugi which is valued by people is originated by the thickness variation of tsumugi yarn, however the detail of the variation is unknown.There must be a law and/or a theorem of the unevenness to give favorable impression by the yarn used in the textile products. It will be helpful to find the law to elevate the producer's technique and the consumer's satisfaction.