Category: Uncategorized

Oct 22

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

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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]

Oct 22

Corrigendum to "Heat Shock Protein 70 and 90 Genes in the Harmful Dinoflagellate Cochlodinium polykrikoides: Genomic Structures and Transcriptional Responses to Environmental Stresses".

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Corrigendum to “Heat Shock Protein 70 and 90 Genes in the Harmful Dinoflagellate Cochlodinium polykrikoides: Genomic Structures and Transcriptional Responses to Environmental Stresses”.
Int J Genomics. 2015…

Oct 11

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

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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, Ullr…

Oct 11

Cryptosporidium parvum IId family: clonal population and dispersal from Western Asia to other geographical regions.

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Cryptosporidium parvum IId family: clonal population and dispersal from Western Asia to other geographical regions.

Sci Rep. 2014;4:4208

Authors: Wang R, Zhang L, Axén C, Bjorkman C, Jian F, Amer S, Liu A, Feng Y, Li G, Lv C, Zhao Z, Qi M, Dong H, Wang H, Sun Y, Ning C, Xiao L

Abstract
In this study, 111 Cryptosporidium parvum IId isolates from several species of animals in China, Sweden, and Egypt were subtyped by multilocus sequence typing (MLST). One to eleven subtypes were detected at each of the 12 microsatellite, minisatellite, and single nucleotide polymorphism (SNP) loci, forming 25 MLST subtypes. Host-adaptation and significant geographical segregation were both observed in the MLST subtypes. A clonal population structure was seen in C. parvum IId isolates from China and Sweden. Three ancestral lineages and the same RPGR sequence were shared by these isolates examined. Therefore, the present genetic observations including the higher nucleotide diversity of C. parvum IId GP60 sequences in Western Asia, as well as the unique distribution of IId subtypes (almost exclusively found in Asia, Europe, and Egypt) and in combination with the domestication history of cattle, sheep, and goats, indicated that C. parvum IId subtypes were probably dispersed from Western Asia to other geographical regions. More population genetic structure studies involving various C. parvum subtype families using high-resolution tools are needed to better elucidate the origin and dissemination of C. parvum in the world.

PMID: 24572610 [PubMed – indexed for MEDLINE]

Oct 07

Microbial Malaise: How Can We Classify the Microbiome?

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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 understa…

Oct 07

Phylogenetic approaches to microbial community classification.

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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]

Oct 07

Archaea.

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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 …

Oct 07

Endosymbiosis and Eukaryotic Cell Evolution.

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Endosymbiosis and Eukaryotic Cell Evolution.

Curr Biol. 2015 Oct 5;25(19):R911-21

Authors: Archibald JM

Abstract
Understanding the evolution of eukaryotic cellular complexity is one of the grand challenges of modern biology. It has now been firmly established that mitochondria and plastids, the classical membrane-bound organelles of eukaryotic cells, evolved from bacteria by endosymbiosis. In the case of mitochondria, evidence points very clearly to an endosymbiont of α-proteobacterial ancestry. The precise nature of the host cell that partnered with this endosymbiont is, however, very much an open question. And while the host for the cyanobacterial progenitor of the plastid was undoubtedly a fully-fledged eukaryote, how – and how often – plastids moved from one eukaryote to another during algal diversification is vigorously debated. In this article I frame modern views on endosymbiotic theory in a historical context, highlighting the transformative role DNA sequencing played in solving early problems in eukaryotic cell evolution, and posing key unanswered questions emerging from the age of comparative genomics.

PMID: 26439354 [PubMed – in process]

Oct 01

Seasonal Preservation Success of the Marine Dinoflagellate Coral Symbiont, Symbiodinium sp.

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Seasonal Preservation Success of the Marine Dinoflagellate Coral Symbiont, Symbiodinium sp.
PLoS One. 2015;10(9):e0136358
Authors: Hagedorn M, Carter VL
Abstract
Coral reefs are som…

Sep 30

The Semantics of the Modular Architecture of Protein Structures.

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The Semantics of the Modular Architecture of Protein Structures.
Curr Protein Pept Sci. 2015 Sep 22;
Authors: Hleap JS, Blouin C
Abstract
Protein structures can be conceptualized as …