Category: Uncategorized

Molecular Organization of the 5s rDna Gene Type II in Elasmobranchs.

RNA Biol. 2015 Oct 21;:0

Authors: Castro SI, Hleap JS, Cárdenas H, Blouin C

Abstract
The 5S rDNA gene is a non-coding RNA that can be found in two copies (type I and type II) in bony and cartilaginous fish. Previous studies have pointed out that type II gene is a paralog derived from type I. We analyzed the molecular organization of 5S rDNA type II in elasmobranchs. Although the structure of the 5S rDNA is supposed to be highly conserved, our results show that the secondary structure in this group possesses some variability and is different than the consensus secondary structure. One of these differences in Selachii is an internal loop at nucleotides 7 and 112. These mutations observed in the transcribed region suggest an independent origin of the gene among Batoids and Selachii. All promoters were highly conserved with the exception of BoxA, possibly due to its affinity to polymerase III. This latter enzyme recognizes a dT4 sequence as stop signal, however in Rajiformes this signal was doubled in length to dT8. This could be an adaptation towards a higher efficiency in the termination process. Our results suggest that there is no TATA box in elasmobranchs in the NTS region. We also provide some evidence suggesting that the complexity of the microsatellites present in the NTS region play an important role in the 5S rRNA gene since it is significantly correlated with the length of the NTS.

PMID: 26488198 [PubMed – as supplied by publisher]

Localization and evolution of putative triose phosphate translocators in the diatom Phaeodactylum tricornutum.

Genome Biol Evol. 2015 Oct 9;

Authors: Moog D, Rensing SA, Archibald JM, Maier UG, Ullrich KK

Abstract
The establishment of a metabolic connection between host and symbiont is a crucial step in the evolution of an obligate endosymbiotic relationship. Such was the case in the evolution of mitochondria and plastids. Whereas the mechanisms of metabolite shuttling between the plastid and host cytosol are relatively well studied in Archaeplastida – organisms that acquired photosynthesis through primary endosymbiosis – little is known about this process in organisms with complex plastids. Here we focus on the presence, localization and phylogeny of putative triose phosphate translocators (TPTs) in the complex plastid of diatoms. These proteins are thought to play an essential role in connecting endosymbiont and host metabolism via transport of carbohydrates generated by the photosynthesis machinery of the endosymbiont. We show that the complex plastid localized TPTs are monophyletic and present a model for how the initial metabolic link between host and endosymbiont might have been established in diatoms and other algae with complex red plastids and discuss its implications on the evolution of those lineages.

PMID: 26454011 [PubMed – as supplied by publisher]

Microbial Malaise: How Can We Classify the Microbiome?

Trends Microbiol. 2015 Sep 19;

Authors: Beiko RG

Abstract
The names and lineages of microorganisms are critical to our understanding of the microbiome. However, microbial taxonomy and phylogeny are in perpetual flux, with emerging criteria being used to rename and reshape our views of the microbial world. Different candidate molecular and nonmolecular criteria are often broadly consistent with one another, which underpins the pluralistic approach to taxonomy. However, the taxonomic picture is clouded when underlying criteria are not in agreement, or when reference datasets contain erroneously named organisms. How does the shifting taxonomic landscape impact our interpretation of microbial communities, especially in the face of inconsistencies and errors? How can taxonomy be applied in a consistent way when different users have different requirements of the classifications that emerge? The key path forward involves finding ways to integrate conflicting taxonomic criteria, choosing the right units of analysis for microbiomic studies, and making molecular taxonomy transparent and accessible in a way that complements current genomic resources.

PMID: 26439295 [PubMed – as supplied by publisher]

Phylogenetic approaches to microbial community classification.

Microbiome. 2015;3(1):47

Authors: Ning J, Beiko RG

Abstract
BACKGROUND: The microbiota from different body sites are dominated by different major groups of microbes, but the variations within a body site such as the mouth can be more subtle. Accurate predictive models can serve as useful tools for distinguishing sub-sites and understanding key organisms and their roles and can highlight deviations from expected distributions of microbes. Good classification depends on choosing the right combination of classifier, feature representation, and learning model. Machine-learning procedures have been used in the past for supervised classification, but increased attention to feature representation and selection may produce better models and predictions.
RESULTS: We focused our attention on the classification of nine oral sites and dental plaque in particular, using data collected from the Human Microbiome Project. A key focus of our representations was the use of phylogenetic information, both as the basis for custom kernels and as a way to represent sets of microbes to the classifier. We also used the PICRUSt software, which draws on phylogenetic relationships to predict molecular functions and to generate additional features for the classifier. Custom kernels based on the UniFrac measure of community dissimilarity did not improve performance. However, feature representation was vital to classification accuracy, with microbial clade and function representations providing useful information to the classifier; combining the two types of features did not yield increased prediction accuracy. Many of the best-performing clades and functions had clear associations with oral microflora.
CONCLUSIONS: The classification of oral microbiota remains a challenging problem; our best accuracy on the plaque dataset was approximately 81 %. Perfect accuracy may be unattainable due to the close proximity of the sites and intra-individual variation. However, further exploration of the space of both classifiers and feature representations is likely to increase the accuracy of predictive models.

PMID: 26437943 [PubMed – in process]

Archaea.

Curr Biol. 2015 Oct 5;25(19):R851-5

Authors: Eme L, Doolittle WF

Abstract
A headline on the front page of the New York Times for November 3, 1977, read “Scientists Discover a Way of Life That Predates Higher Organisms”. The accompanying article described a spectacular claim by Carl Woese and George Fox to have discovered a third form of life, a new ‘domain’ that we now call Archaea. It’s not that these microbes were unknown before, nor was it the case that their peculiarities had gone completely unnoticed. Indeed, Ralph Wolfe, in the same department at the University of Illinois as Woese, had already discovered how it was that methanogens (uniquely on the planet) make methane, and the bizarre adaptations that allow extremely halophilic archaea (then called halobacteria) and thermoacidophiles to live in the extreme environments where they do were already under investigation in many labs. But what Woese and Fox had found was that these organisms were related to each other not just in their ‘extremophily’ but also phylogenetically. And, most surprisingly, they were only remotely related to the rest of the prokaryotes, which we now call the domain Bacteria (Figure 1).

PMID: 26439345 [PubMed – in process]