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The transcription initiation landscape of eukaryotic genes is complex and highly dynamic. In eukaryotes, genes can generate multiple transcript variants that differ in 5′ boundaries due to usages of alternative transcription start sites (TSSs), and the abundance of transcript isoforms are highly variable. Due to a large number and complexity of the TSSs, it is not feasible to depict details of transcript initiation landscape of all genes using text-format genome annotation files. Therefore, it is necessary to provide data visualization of TSSs to represent quantitative TSS maps and the core promoters (CPs). In addition, the selection and activity of TSSs are influenced by various factors, such as transcription factors, chromatin remodeling and histone modifications. Thus, integration and visualization of functional genomic data related to these features could provide a better understanding of the gene promoter architecture and regulatory mechanism of transcription initiation. Yeast species play important roles for the research and human society, yet no database provides visualization and integration of functional genomic data in yeast. Here, we generated quantitative TSS maps for 12 important yeast species, inferred their CPs and built a public database, YeasTSS (www.yeastss.org). YeasTSS was designed as a central portal for visualization and integration of the TSS maps, CPs and functional genomic data related to transcription initiation in yeast. YeasTSS is expected to benefit the research community and public education for improving genome annotation, studies of promoter structure, regulated control of transcription initiation and inferring gene regulatory network.

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Numerical study of dynamic relaxation with kinetic damping applied to inflatable fabric structures with extensions for 3D solid element and non-linear behavior. Thin-Walled Structures, Elsevier, 2011, 49 (11) This work mainly deals with the numerical study of inflatable fabric structures. As implicit integration schemes can lead to numerical difficulties such as singular stiffness matrices, explicit schemes are preferred. Since the final objective of this study is to obtain the final shape of a structure, a dynamic relaxation (DR) method is used. These methods allow us to obtain the final and stable shape of the inflatable fabric structures without doing so many time increments, which is the case when using a classical explicit integration method. Han and Lee [5] proposed an extension of the DR method stated by Barnes [13] suitable for triangular elements and elastic behavior. There are two main contributions in this paper. Firstly, we propose a modification of Han and Lee's method, allowing it to be used with any kind of membrane or solid finite elements and any reversible behavior. Secondly, we propose to rewrite the expression initially introduced by Barnes. Furthermore, these proposals are adapted for incremental loadings, allowing this way to obtain the pseudo-equilibriums of the intermediate phases.Numerical examples from academic problems (rectangular and circular membranes) show the efficiency and the reliability of proposed methods, with linear elasticity behavior, and also with a non-linear incremental behavior and finite deformation states.

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9Ribosomal proteins (RPs) genes encode structure components of ribosomes, the cellular 2 0 machinery for protein synthesis. A single functional copy has been maintained in most of 78-80 2 1 RP families in animals due to evolutionary constraints imposed by gene dosage balance. Some 2 2 fungal species have maintained duplicate copies in most RP families. How the RP genes were 2 3 duplicated and maintained in these fungal species, and their functional significance remains 2 4 unresolved. To address these questions, we identified all RP genes from 295 fungi and inferred 2 5 the timing and nature of gene duplication for all RP families. We found that massive duplications 2 6 of RP genes have independently occurred by different mechanisms in three distantly related 2 7 lineages. The RP duplicates in two of them, budding yeast and Mucoromycota, were mainly 2 8 created by whole genome duplication (WGD) events. However, in fission yeasts, duplicate RP 2 9 genes were likely generated by retroposition, which is unexpected considering their dosage 3 0 sensitivity. The sequences of most RP paralogs in each species have been homogenized by 3 1 repeated gene conversion, demonstrating parallel concerted evolution, which might have 3 2 facilitated the retention of their duplicates. Transcriptomic data suggest that the duplication and 3 3 retention of RP genes increased RP transcription abundance. Physiological data indicate that 3 4increased ribosome biogenesis allowed these organisms to rapidly consuming sugars through 3 5 fermentation while maintaining high growth rates, providing selective advantages to these 3 6 species in sugar-rich environments.

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