Author's posts
Mar 21
megasat: automated inference of microsatellite genotypes from sequence data.
megasat is software that enables genotyping of microsatellite loci using next-generation sequencing data. Microsatellites are amplified in large multiplexes, and then sequenced in pooled amplicons. megasat reads sequence files and automatically scores microsatellite genotypes. It uses fuzzy matches to allow for sequencing errors and applies decision rules to account for amplification artefacts, including nontarget amplification …
Mar 21
Discovery of an expanded set of avian leukosis subroup E proviruses in chickens using Vermillion, a novel sequence capture and analysis pipeline.
Transposable elements (TEs), such as endogenous retroviruses (ERVs), are common in the genomes of vertebrates. ERVs result from retroviral infections of germ-line cells, and once integrated into host DNA they become part of the host’s heritable genetic material. ERVs have been ascribed positive effects on host physiology such as the generation of novel, adaptive genetic …
Mar 21
Genomic Analysis of a Serotype 5 Streptococcus pneumoniae Outbreak in British Columbia, Canada, 2005-2009.
Background. Streptococcus pneumoniae can cause a wide spectrum of disease, including invasive pneumococcal disease (IPD). From 2005 to 2009 an outbreak of IPD occurred in Western Canada, caused by a S. pneumoniae strain with multilocus sequence type (MLST) 289 and serotype 5. We sought to investigate the incidence of IPD due to this S. pneumoniae …
Mar 21
Osmoadaptative Strategy and Its Molecular Signature in Obligately Halophilic Heterotrophic Protists.
Halophilic microbes living in hypersaline environments must counteract the detrimental effects of low water activity and salt interference. Some halophilic prokaryotes equilibrate their intracellular osmotic strength with the extracellular milieu by importing inorganic solutes, mainly potassium. These “salt-in” organisms characteristically have proteins that are highly enriched with acidic and hydrophilic residues. In contrast, “salt-out” halophiles …
Mar 21
On the reversibility of parasitism: adaptation to a free-living lifestyle via gene acquisitions in the diplomonad Trepomonas sp. PC1.
BACKGROUND: It is generally thought that the evolutionary transition to parasitism is irreversible because it is associated with the loss of functions needed for a free-living lifestyle. Nevertheless, free-living taxa are sometimes nested within parasite clades in phylogenetic trees, which could indicate that they are secondarily free-living. Herein, we test this hypothesis by studying the …
Mar 15
The Modern Synthesis in the Light of Microbial Genomics.
We review the theoretical implications of findings in genomics for evolutionary biology since the Modern Synthesis. We examine the ways in which microbial genomics has influenced our understanding of the last universal common ancestor, the tree of life, species, lineages, and evolutionary transitions. We conclude by advocating a piecemeal toolkit approach to evolutionary biology, in …
Mar 15
Erratum to: On the reversibility of parasitism: adaptation to a free-living lifestyle via gene acquisitions in the diplomonad Trepomonas sp. PC1.
Warning: The NCBI web site requires JavaScript to function. more… Result Filters See comment in PubMed Commons below Xu F1, Jerlström-Hultqvist J1,2, Kolisko M3,4,5, Simpson AG3,6, Roger AJ4,6, Svärd SG1, Andersson JO7. Author information 1 Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden. 2 Present address: Department of Medical …
Mar 15
Arginine deiminase pathway enzymes: evolutionary history in metamonads and other eukaryotes.
BACKGROUND: Multiple prokaryotic lineages use the arginine deiminase (ADI) pathway for anaerobic energy production by arginine degradation. The distribution of this pathway among eukaryotes has been thought to be very limited, with only two specialized groups living in low oxygen environments (Parabasalia and Diplomonadida) known to possess the complete set of all three enzymes. We …
Mar 15
The Gut Microbiome of Pediatric Crohn’s Disease Patients Differs from Healthy Controls in Genes That Can Influence the Balance Between a Healthy and Dysregulated Immune Response.
BACKGROUND: Exclusive enteral nutrition (EEN) is a first-line therapy in pediatric Crohn’s disease (CD) thought to induce remission through changes in the gut microbiome. With microbiome assessment largely focused on microbial taxonomy and diversity, it remains unclear to what extent EEN induces functional changes that thereby contribute to its therapeutic effect. METHODS: Fecal samples were …
Mar 15
Early Changes in Microbial Community Structure Are Associated with Sustained Remission After Nutritional Treatment of Pediatric Crohn’s Disease.
BACKGROUND: Clinical remission achieved by exclusive enteral nutrition (EEN) is associated with marked microbiome changes. In this prospective study of exclusive enteral nutrition, we employ a hierarchical model of microbial community structure to distinguish between pediatric Crohn’s disease patients who achieved sustained remission (SR) and those who relapsed early (non-SR), after restarting a normal diet. …
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