01.06.2013 | Nuno S. Osório; Fernando Rodrigues; Sebastien Gagneux; Jorge Pedrosa; Marta Pinto-Carbó; António G. Castro; Douglas ..., Molecular Biology and Evolution, 2013

Tuberculosis (TB) is a global health problem estimated to kill 1.4 million people per year. Recent advances in the genomics of the causative agents of TB, bacteria known as the Mycobacterium tuberculosis complex (MTBC), have allowed a better comprehension of its population structure and ...

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01.06.2013 | Marie Filteau; Scott A. Pavey; Jérôme St-Cyr; Louis Bernatchez, Molecular Biology and Evolution, 2013

A functional understanding of processes involved in adaptive divergence is one of the awaiting opportunities afforded by high-throughput transcriptomic technologies. Functional analysis of coexpressed genes has succeeded in the biomedical field in identifying key drivers of disease pathways. ...

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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 | Pieter Meysman; Aminael Sánchez-Rodríguez; Qiang Fu; Kathleen Marchal; Kristof Engelen, Molecular Biology and Evolution, 2013

Escherichia coli K12 is a commensal bacteria and one of the best-studied model organisms. Salmonella enterica serovar Typhimurium, on the other hand, is a facultative intracellular pathogen. These two prokaryotic species can be considered related phylogenetically, and they share a large ...

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01.06.2013 | Sarah L. Maguire; Seán S. ÓhÉigeartaigh; Kevin P. Byrne; Markus S. Schröder; Peadar O’Gaora; Kenneth H. Wolfe; Geral ..., Molecular Biology and Evolution, 2013

The Candida Gene Order Browser (CGOB) was developed as a tool to visualize and analyze synteny relationships in multiple Candida species, and to provide an accurate, manually curated set of orthologous Candida genes for evolutionary analyses. Here, we describe major improvements to CGOB. The ...

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01.06.2013 | Paolo Innocenti; Stephen F. Chenoweth, Molecular Biology and Evolution, 2013

Change in gene expression is a major facilitator of phenotypic evolution. Understanding the evolutionary potential of gene expression requires taking into account complex systems of regulatory networks, the structure of which could potentially bias evolutionary trajectories. We analyzed the ...

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01.06.2013 | Rachele Cagliani; Diego Forni; Stefania Riva; Uberto Pozzoli; Marta Colleoni; Nereo Bresolin; Mario Clerici; Manuela ..., Molecular Biology and Evolution, 2013

Activation of the contact system leads to the cleavage of kininogen by plasma kallikrein resulting in kinin release and in the initiation of the intrinsic pathway of coagulation. Proteolysis of kininogen also generates antimicrobial peptides (AMPs) and can be induced by diverse pathogens. ...

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01.06.2013 | Etienne Simon-Loriere; Edward C. Holmes, Molecular Biology and Evolution, 2013

Gene duplication generates genetic novelty and redundancy and is a major mechanism of evolutionary change in bacteria and eukaryotes. To date, however, gene duplication has been reported only rarely in RNA viruses. Using a conservative BLAST approach we systematically screened for the ...

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01.06.2013 | Sujay Chattopadhyay; Fred Taub; Sandip Paul; Scott J. Weissman; Evgeni V. Sokurenko, Molecular Biology and Evolution, 2013

Analysis of genetic differences (gene presence/absence and nucleotide polymorphisms) among strains of a bacterial species is crucial to understanding molecular mechanisms of bacterial pathogenesis and selecting targets for novel antibacterial therapeutics. However, lack of genome-wide ...

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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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