March 2015 archive

Mar 31

Ultrastructure and molecular phylogenetic position of Neometanema parovale sp. nov. (Neometanema gen. nov.), a Marine phagotrophic euglenid with skidding motility.

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Ultrastructure and molecular phylogenetic position of Neometanema parovale sp. nov. (Neometanema gen. nov.), a Marine phagotrophic euglenid with skidding motility.

Protist. 2014 Aug;165(4):452-72

Authors: Lee WJ, Simpson AG

Abstract
Heteronema is a commonly encountered genus of phagotrophic euglenids that contains very different morphotypes, including elongate gliding species and ovoid skidding forms. We report the first ultrastructural and sequence data from a culture of an ovoid skidding heteronemid, KM051. Cells were 8-23.5 μm long with 22 pellicular strips and a fibrous extracellular layer. The tubular extrusomes had dense centre sections. The feeding apparatus was barely visible by light microscopy, but included two microtubule-supported rods. The flagella had hollow, inflated transition zones, heteromorphic paraxonemal rods, and sheaths of flagellar hairs. The posterior flagellum bore a knob that, unusually, sat >2 μm distal to the flagellar base. No ultrastructural features were uniquely shared by KM051 and the elongate, gliding species Heteronema scaphurum. Conversely, the pellicular microtubule array resembles that in deep-branching primary osmotrophs (Aphagea). 18S ribosomal DNA (18S rDNA) phylogenies showed that KM051 is related to a recently obtained Heteronema c.f. exaratum sequence. These skidding heteronemids are not closely related to H. scaphurum, and instead are closely related to Dinema, Anisonema and specifically, Aphagea. The skidding species in Heteronema are transferred to Neometanema gen. nov. (along with most species of Metanema Klebs, 1893), with KM051 described as Neometanema parovale sp. nov.

PMID: 24945929 [PubMed – indexed for MEDLINE]

Mar 31

Creneis carolina gen. et sp. nov. (Heterolobosea), a novel marine anaerobic protist with strikingly derived morphology and life cycle.

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Creneis carolina gen. et sp. nov. (Heterolobosea), a novel marine anaerobic protist with strikingly derived morphology and life cycle.

Protist. 2014 Aug;165(4):542-67

Authors: Pánek T, Simpson AG, Hampl V, Cepička I

Abstract
We report the light-microscopic morphology and ultrastructure of a novel free-living, heterotrophic protist, Creneis carolina gen. et sp. nov. isolated from marine anoxic sediments. C. carolina is a heterotrophic, obligately anaerobic amoeboid flagellate, and superficially resembles Mastigamoeba (Amoebozoa: Archamoebae) or Breviata (Breviatea) by possessing a single anterior flagellum closely associated with the nucleus, and because it appears to be an anaerobe. However, its life cycle contains multiflagellate cells with an unusual morphology. The structure of the mastigont of C. carolina is unique and not readily comparable with any eukaryotic group. Unexpectedly, phylogenetic analyses of SSU rDNA and of a concatenate of α- and β-tubulin genes with SSU rDNA convincingly showed that C. carolina is a member of Heterolobosea and belongs to the taxon Tetramitia.

PMID: 24999602 [PubMed – indexed for MEDLINE]

Mar 20

Microbial diversity: a bonanza of phyla.

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Microbial diversity: a bonanza of phyla.
Curr Biol. 2015 Mar 16;25(6):R227-30
Authors: Eme L, Doolittle WF
Abstract
Metagenomics and single-cell genomics are now the gold standard fo…

Mar 19

Intra-genomic variation in symbiotic dinoflagellates: recent divergence or recombination between lineages?

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Intra-genomic variation in symbiotic dinoflagellates: recent divergence or recombination between lineages?

BMC Evol Biol. 2015 Dec;15(1):325

Authors: Wilkinson SP, Fisher PL, van Oppen MJ, Davy SK

Abstract
BACKGROUND: The symbiosis between corals and the dinoflagellate alga Symbiodinium is essential for the development and survival of coral reefs. Yet this fragile association is highly vulnerable to environmental disturbance. A coral’s ability to tolerate temperature stress depends on the fitness of its resident symbionts, whose thermal optima vary extensively between lineages. However, the in hospite population genetic structure of Symbiodinium is poorly understood and mostly based on analysis of bulk DNA extracted from thousands to millions of cells. Using quantitative single-cell PCR, we enumerated DNA polymorphisms in the symbionts of the reef-building coral Pocillopora damicornis, and applied a model selection approach to explore the potential for recombination between coexisting Symbiodinium populations.
RESULTS: Two distinct Symbiodinium ITS2 sequences (denoted C100 and C109) were retrieved from all P. damicornis colonies analysed. However, the symbiont assemblage consisted of three distinct Symbiodinium populations: cells featuring pure arrays of ITS2 type C109, near-homogeneous cells of type C100 (with trace ITS2 copies of type C109), and those with co-dominant C100 and C109 ITS2 repeats. The symbiont consortia of some colonies consisted almost entirely of these putative C100 × C109 recombinants.
CONCLUSIONS: Our results are consistent with the occurrence of sexual recombination between Symbiodinium types C100 and C109. While the multiple-copy nature of the ITS2 dictates that the observed pattern of intra-genomic co-dominance may be a result of incomplete concerted evolution of intra-genomic polymorphisms, this is a less likely explanation given the occurrence of homogeneous cells of the C109 type. Conclusive evidence for inter-lineage recombination and introgression in this genus will require either direct observational evidence or a single-cell genotyping approach targeting multiple, single-copy loci.

PMID: 25776334 [PubMed – in process]

Mar 17

BioMiCo: a supervised Bayesian model for inference of microbial community structure.

BioMiCo: a supervised Bayesian model for inference of microbial community structure.
Microbiome. 2015;3:8
Authors: Shafiei M, Dunn KA, Boon E, MacDonald SM, Walsh DA, Gu H, Bielawski JP
Abstract
BAC…

Mar 14

Alternatives to vitamin B1 uptake revealed with discovery of riboswitches in multiple marine eukaryotic lineages.

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Alternatives to vitamin B1 uptake revealed with discovery of riboswitches in multiple marine eukaryotic lineages.
ISME J. 2014 Dec;8(12):2517-29
Authors: McRose D, Guo J, Monier A, Sudek S, Wilken…

Mar 11

Organelle evolution, fragmented rRNAs, and Carl.

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Organelle evolution, fragmented rRNAs, and Carl.
RNA Biol. 2014 Mar;11(3):213-6
Authors: Gray MW
Abstract
I am honored to have been asked to contribute to this memorial issue, alth…

Mar 11

Phylogenomic analysis of Emiliania huxleyi provides evidence for haptophyte-stramenopile association and a chimeric haptophyte nuclear genome.

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Phylogenomic analysis of Emiliania huxleyi provides evidence for haptophyte-stramenopile association and a chimeric haptophyte nuclear genome.
Mar Genomics. 2015 Mar 4;
Authors: Miller JJ, Delwiche …

Mar 07

Diversification of the Light-Harvesting Complex Gene Family via Intra- and Intergenic Duplications in the Coral Symbiotic Alga Symbiodinium.

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Diversification of the Light-Harvesting Complex Gene Family via Intra- and Intergenic Duplications in the Coral Symbiotic Alga Symbiodinium.
PLoS One. 2015;10(3):e0119406
Authors: Maruyama S, Shogu…

Mar 07

Whole-of-society approach for public health policymaking: a case study of polycentric governance from Quebec, Canada.

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Whole-of-society approach for public health policymaking: a case study of polycentric governance from Quebec, Canada.

Ann N Y Acad Sci. 2014 Dec;1331:216-29

Authors: Addy NA, Poirier A, Blouin C, Drager N, Dubé L

Abstract
In adopting a whole-of-society (WoS) approach that engages multiple stakeholders in public health policies across contexts, the authors propose that effective governance presents a challenge. The purpose of this paper is to highlight a case for how polycentric governance underlying the WoS approach is already functioning, while outlining an agenda to enable adaptive learning for improving such governance processes. Drawing upon a case study from Quebec, Canada, we employ empirically developed concepts from extensive, decades-long work of the 2009 Nobel laureate Elinor Ostrom in the governance of policy in nonhealth domains to analyze early efforts at polycentric governance in policies around overnutrition, highlighting interactions between international, domestic, state and nonstate actors and processes. Using information from primary and secondary sources, we analyze the emergence of the broader policy context of Quebec’s public health system in the 20th century. We present a microsituational analysis of the WoS approach for Quebec’s 21st century policies on healthy lifestyles, emphasizing the role of governance at the community level. We argue for rethinking prescriptive policy analysis of the 20th century, proposing an agenda for diagnostic policy analysis, which explicates the multiple sets of actors and interacting variables shaping polycentric governance for operationalizing the WoS approach to policymaking in specific contexts.

PMID: 25118135 [PubMed – indexed for MEDLINE]