01.06.2013 | Mélisande Blein-Nicolas; Warren Albertin; Benoît Valot; Philippe Marullo; Delphine Sicard; Christophe Giraud; Sylvie ..., Molecular Biology and Evolution, 2013

Saccharomyces cerevisiae and S. uvarum are two domesticated species of the Saccharomyces sensu stricto clade that diverged around 100 Ma after whole-genome duplication. Both have retained many duplicated genes associated with glucose fermentation and are characterized by the ability to ...

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01.06.2013 | Zhang Wang; Martin Wu, Molecular Biology and Evolution, 2013

Large-scale, genome-level molecular phylogenetic analyses present both opportunities and challenges for bacterial evolutionary and ecological studies. We constructed a phylum-level bacterial phylogenetic marker database by surveying all complete bacterial genomes and identifying single-copy ...

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01.06.2013 | Manuel Gil; Marcelo Serrano Zanetti; Stefan Zoller; Maria Anisimova, Molecular Biology and Evolution, 2013

Markov models of codon substitution naturally incorporate the structure of the genetic code and the selection intensity at the protein level, providing a more realistic representation of protein-coding sequences compared with nucleotide or amino acid models. Thus, for protein-coding genes, ...

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01.06.2013 | Masahiko Yabu; Hiroaki Korekane; Koji Hatano; Yasufumi Kaneda; Norio Nonomura; Chihiro Sato; Ken Kitajima; Yasuhide ..., Glycobiology , 2013

We previously reported on the accumulation of a substantial amount of free N-acetylneuraminic acid (Neu5Ac)-containing complex-type N-glycans in human pancreatic cancer cells (Yabu M, Korekane H, Takahashi H, Ohigashi H, Ishikawa O, Miyamoto Y. 2013. Accumulation of free Neu5Ac-containing ...

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17.05.2013 | Jin Lü, Xiaodan Wu, Yali Jiang, Xiaofeng Cai, Luyao Huang, Yongbo Yang, Huili Wang, Aibing Zeng, Aiying Li, Journal of Basic Microbiology, 2013

Abstract Extremophiles are potential resources for alkaline protease production. In order to search for alkaline protease producers, we isolated and screened alkaliphilic microorganisms from alkaline saline environments. The microorganism HSL10 was identified as a member of the genus ...

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16.05.2013 | Julian Garrec et al., PLoS Computational Biology, 2013

by Julian Garrec, Ivano Tavernelli, Ursula Rothlisberger Using molecular dynamics simulations, we show that the prion protein (PrP) exhibits a dual behavior, with two possible transition routes, upon protonation of H187 around pH 4.5, which mimics specific conditions encountered in ...

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16.05.2013 | Christoph A. Haselwandter et al., PLoS Computational Biology, 2013

by Christoph A. Haselwandter, Rob Phillips The mechanosensitive channel of large conductance (MscL) is capable of transducing mechanical stimuli such as membrane tension into an electrochemical response. MscL provides a widely-studied model system for mechanotransduction and, more ...

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16.05.2013 | Vincent Vagenende et al., PLoS Computational Biology, 2013

by Vincent Vagenende, Alvin X. Han, Han B. Pek, Bernard L. W. Loo Although the nature of solvent-protein interactions is generally weak and non-specific, addition of cosolvents such as denaturants and osmolytes strengthens protein-protein interactions for some proteins, whereas it weakens ...

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15.05.2013 | Nohemi Carreras‐Villaseñor, Edgardo U. Esquivel‐Naranjo, J. Manuel Villalobos‐Escobedo, Cei Abreu‐Goodger, Alfredo H ..., Molecular Microbiology, 2013

Summary The RNAi machinery is generally involved in genome protection in filamentous fungi, however the physiological role of RNAi has been poorly studied in fungal models. Here, we report that in the filamentous fungus Trichoderma atroviride, the products of the dcr2 and rdr3 genes ...

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15.05.2013 | Hai Dang Nguyen, Sandra Studenik, Gabriele Diekert, FEMS Microbiology Letters, 2013

Abstract The O‐demethylases of anaerobes are corrinoid‐dependent, ether‐cleaving methyltransferase enzyme systems consisting of four components. The interaction of the O‐demethylase components of the acetogenic bacterium Acetobacterium dehalogenans was studied by protein mobility on ...

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