Author's posts

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 …

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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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Mar 15

Probing the evolution, ecology and physiology of marine protists using transcriptomics.

Protists, which are single-celled eukaryotes, critically influence the ecology and chemistry of marine ecosystems, but genome-based studies of these organisms have lagged behind those of other microorganisms. However, recent transcriptomic studies of cultured species, complemented by meta-omics analyses of natural communities, have increased the amount of genetic information available for poorly represented branches on the …

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Mar 15

Molecular Phylogenetics and the Perennial Problem of Homology.

The concept of homology has a long history, during much of which the issue has been how to reconcile similarity and common descent when these are not coextensive. Although thinking molecular phylogeneticists have learned not to say “percent homology,” the problems are deeper than that and unresolved.

Mar 15

Microbial Evolution: Xenology (Apparently) Trumps Paralogy.

Within-genome gene duplication is generally considered the source of extra copies when higher dosage is required and a starting point for evolution of new function. A new study suggests that horizontal gene transfer can appear to play both roles. Copyright © 2016 Elsevier Ltd. All rights reserved.

Mar 15

Scaling Up the Phylogenetic Detection of Lateral Gene Transfer Events.

Lateral genetic transfer (LGT) is the process by which genetic material moves between organisms (and viruses) in the biosphere. Among the many approaches developed for the inference of LGT events from DNA sequence data, methods based on the comparison of phylogenetic trees remain the gold standard for many types of problem. Identifying LGT events from …

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Mar 15

Evolution: Plumbing the Depths of Diplonemid Diversity.

Environmental molecular sequence surveys have opened a window on the hidden riches of the microbial biosphere. Recent genetic ‘barcoding’ and single-cell genomics studies have provided a snapshot of the biology of diplonemids – abundant, diverse, marine heterotrophic protists whose ecological roles are becoming clearer. Copyright © 2016 Elsevier Ltd. All rights reserved.

Mar 15

Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research.

Sequence-based approaches to study microbiomes, such as 16S rRNA gene sequencing and metagenomics, are uncovering associations between microbial taxa and a myriad of factors. A drawback of these approaches is that the necessary sequencing library preparation and bioinformatic analyses are complicated and continuously changing, which can be a barrier for researchers new to the field. …

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Mar 15

Gregarine infection accelerates larval development of the cat flea Ctenocephalides felis (Bouché).

A high degree of specialization between host and parasite is a well-known outcome of a long history of coevolution, and it is strikingly illustrated in a coordination of their life cycles. In some cases, the arms race ensued at the establishment of a symbiotic relationship results in the adoption of manipulative strategies by the parasite. …

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Mar 15

The origin of mitochondrial cristae from alphaproteobacteria.

Mitochondria are the respiratory organelles of eukaryotes and their evolutionary history is deeply intertwined with that of eukaryotes. The compartmentalization of respiration in mitochondria occurs within cristae, whose evolutionary origin has remained unclear. Recent discoveries, however, have revived the old notion that mitochondrial cristae could have had a pre-endosymbiotic origin. Mitochondrial cristae are likely homologous …

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