October 2014 archive

Oct 31

Rhodoluna lacicola gen. nov., sp. nov., a planktonic freshwater bacterium with stream-lined genome.

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Rhodoluna lacicola gen. nov., sp. nov., a planktonic freshwater bacterium with stream-lined genome.

Int J Syst Evol Microbiol. 2014 Sep;64(Pt 9):3254-63

Authors: Hahn MW, Schmidt J, Taipale SJ, Doolittle WF, Koll U

Abstract
A pure culture of an actinobacterium previously described as ‘Candidatus Rhodoluna lacicola’ strain MWH-Ta8 was established and deposited in two public culture collections. Strain MWH-Ta8(T) represents a free-living planktonic freshwater bacterium obtained from hypertrophic Meiliang Bay, Lake Taihu, PR China. The strain was characterized by phylogenetic and taxonomic investigations, as well as by determination of its complete genome sequence. Strain MWH-Ta8(T) is noticeable due to its unusually low values of cell size (0.05 µm(3)), genome size (1.43 Mbp), and DNA G+C content (51.5 mol%). Phylogenetic analyses based on 16S rRNA gene and RpoB sequences suggested that strain MWH-Ta8(T) is affiliated with the family Microbacteriaceae with Pontimonas salivibrio being its closest relative among the currently described species within this family. Strain MWH-Ta8(T) and the type strain of Pontimonas salivibrio shared a 16S rRNA gene sequence similarity of 94.3 %. The cell-wall peptidoglycan of strain MWH-Ta8(T) was of type B2β (B10), containing 2,4-diaminobutyric acid as the diamino acid. The predominant cellular fatty acids were anteiso-C15 : 0 (36.5 %), iso-C16 : 0 (16.5 %), iso-C15 : 0 (15.6 %) and iso-C14 : 0 (8.9 %), and the major (>10 %) menaquinones were MK-11 and MK-12. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The combined phylogenetic, phenotypic and chemotaxonomic data clearly suggest that strain MWH-Ta8(T) represents a novel species of a new genus in the family Microbacteriaceae, for which the name Rhodoluna lacicola gen. nov., sp. nov. is proposed. The type strain of the type species is MWH-Ta8(T) ( = DSM 23834(T) = LMG 26932(T)).

PMID: 24984700 [PubMed – indexed for MEDLINE]

Oct 29

A phylogenomic view of ecological specialization in the Lachnospiraceae, a family of digestive tract-associated bacteria.

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A phylogenomic view of ecological specialization in the Lachnospiraceae, a family of digestive tract-associated bacteria.
Genome Biol Evol. 2014 Mar;6(3):703-13
Authors: Meehan CJ, Beiko RG
…

Oct 29

Microsatellite abundance across the Anthozoa and Hydrozoa in the phylum Cnidaria.

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Microsatellite abundance across the Anthozoa and Hydrozoa in the phylum Cnidaria.
BMC Genomics. 2014 Oct 27;15(1):939
Authors: Ruiz-Ramos DV, Baums IB
Abstract
BACKGROUND: Microsate…

Oct 25

Unfolding the secrets of coral-algal symbiosis.

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Unfolding the secrets of coral-algal symbiosis.

ISME J. 2014 Oct 24;

Authors: Rosic N, Ling EY, Chan CK, Lee HC, Kaniewska P, Edwards D, Dove S, Hoegh-Guldberg O

Abstract
Dinoflagellates from the genus Symbiodinium form a mutualistic symbiotic relationship with reef-building corals. Here we applied massively parallel Illumina sequencing to assess genetic similarity and diversity among four phylogenetically diverse dinoflagellate clades (A, B, C and D) that are commonly associated with corals. We obtained more than 30 000 predicted genes for each Symbiodinium clade, with a majority of the aligned transcripts corresponding to sequence data sets of symbiotic dinoflagellates and <2% of sequences having bacterial or other foreign origin. We report 1053 genes, orthologous among four Symbiodinium clades, that share a high level of sequence identity to known proteins from the SwissProt (SP) database. Approximately 80% of the transcripts aligning to the 1053 SP genes were unique to Symbiodinium species and did not align to other dinoflagellates and unrelated eukaryotic transcriptomes/genomes. Six pathways were common to all four Symbiodinium clades including the phosphatidylinositol signaling system and inositol phosphate metabolism pathways. The list of Symbiodinium transcripts common to all four clades included conserved genes such as heat shock proteins (Hsp70 and Hsp90), calmodulin, actin and tubulin, several ribosomal, photosynthetic and cytochrome genes and chloroplast-based heme-containing cytochrome P450, involved in the biosynthesis of xanthophylls. Antioxidant genes, which are important in stress responses, were also preserved, as were a number of calcium-dependent and calcium/calmodulin-dependent protein kinases that may play a role in the establishment of symbiosis. Our findings disclose new knowledge about the genetic uniqueness of symbiotic dinoflagellates and provide a list of homologous genes important for the foundation of coral-algal symbiosis.The ISME Journal advance online publication, 24 October 2014; doi:10.1038/ismej.2014.182.

PMID: 25343511 [PubMed – as supplied by publisher]

Oct 22

Separate Introns Gained within Short and Long Soluble Peridinin-Chlorophyll a-Protein Genes during Radiation of Symbiodinium (Dinophyceae) Clade A and B Lineages.

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Separate Introns Gained within Short and Long Soluble Peridinin-Chlorophyll a-Protein Genes during Radiation of Symbiodinium (Dinophyceae) Clade A and B Lineages.
PLoS One. 2014;9(10):e110608
Author…

Oct 18

Survey of the parasite Toxoplasma gondii in human consumed ovine meat in Tunis City.

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Survey of the parasite Toxoplasma gondii in human consumed ovine meat in Tunis City.
PLoS One. 2014;9(1):e85044
Authors: Boughattas S, Ayari K, Sa T, Aoun K, Bouratbine A
Abstract
…

Oct 17

Reduced nuclear genomes maintain high gene transcription levels.

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Reduced nuclear genomes maintain high gene transcription levels.
Mol Biol Evol. 2014 Mar;31(3):625-35
Authors: Tanifuji G, Onodera NT, Moore CE, Archibald JM
Abstract
Reductive geno…

Oct 17

RNA sequencing and de novo assembly of the digestive gland transcriptome in Mytilus galloprovincialis fed with toxinogenic and non-toxic strains of Alexandrium minutum.

RNA sequencing and de novo assembly of the digestive gland transcriptome in Mytilus galloprovincialis fed with toxinogenic and non-toxic strains of Alexandrium minutum.
BMC Res Notes. 2014 Oct 14;7(1):722
Authors: …

Oct 11

Mitochondrial tRNA 5'-editing in Dictyostelium discoideum and Polysphondylium pallidum.

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Mitochondrial tRNA 5′-editing in Dictyostelium discoideum and Polysphondylium pallidum.
J Biol Chem. 2014 May 30;289(22):15155-65
Authors: Abad MG, Long Y, Kinchen RD, Schindel ET, Gray MW, Jackman…

Oct 11

Gene expression and molecular evolution of sxtA4 in a saxitoxin producing dinoflagellate Alexandrium catenella.

Gene expression and molecular evolution of sxtA4 in a saxitoxin producing dinoflagellate Alexandrium catenella.
Toxicon. 2014 Oct 6;
Authors: Wiese M, Murray SA, Alvin A, Neilan BA
Abstract
Dinoflag…