Author's posts
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]
Mar 07
From policy coherence to 21st century convergence: a whole-of-society paradigm of human and economic development.
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From policy coherence to 21st century convergence: a whole-of-society paradigm of human and economic development.
Ann N Y Acad Sci. 2014 Dec;1331:201-15
Authors: Dubé L, Addy NA, Blouin C, Drager N
Abstract
The 20th century saw accelerated human and economic development, with increased convergence in income, wealth, and living standards around the world. For a large part, owing to the well-entrenched Western-centric linear and siloed industrialization pattern, this positive transformation has also been associated with complex societal challenges at the nexus of agricultural, industrial, and health sectors. Efforts at cross-sectoral policy coherence have been deployed with limited success. To go beyond what has been possible thus far, the whole-of-society (WoS) paradigm for human and economic development proposes a 21st century convergence where, instead of the rest (of the world) converging with the West, sectoral and cross-sectoral efforts converge in their single and collective policy and action on a common target of human and economic development. In this paper, we first review and discuss contributions and limitations of policy coherence approaches. We then elaborate the institutional foundation of the WoS paradigm, taking as an anchor the well-established model of polycentric governance that views individuals, and state, market, and community, forming society as part of the same complex adaptive system. Actors within such systems self-organize into nested hierarchies that operate at multiple scales and move toward 21st century convergence of human and economic development.
PMID: 25146105 [PubMed – indexed for MEDLINE]
Feb 27
Factors mediating plastid dependency and the origins of parasitism in apicomplexans and their close relatives.
Factors mediating plastid dependency and the origins of parasitism in apicomplexans and their close relatives.
Proc Natl Acad Sci U S A. 2015 Feb 25;
Authors: Janouškovec J, Tikhonenkov DV, Burki F, Howe AT, Kolísko M, Mylnikov AP, Keeling PJ
Abstract
Apicomplexans are a major lineage of parasites, including causative agents of malaria and toxoplasmosis. How such highly adapted parasites evolved from free-living ancestors is poorly understood, particularly because they contain nonphotosynthetic plastids with which they have a complex metabolic dependency. Here, we examine the origin of apicomplexan parasitism by resolving the evolutionary distribution of several key characteristics in their closest free-living relatives, photosynthetic chromerids and predatory colpodellids. Using environmental sequence data, we describe the diversity of these apicomplexan-related lineages and select five species that represent this diversity for transcriptome sequencing. Phylogenomic analysis recovered a monophyletic lineage of chromerids and colpodellids as the sister group to apicomplexans, and a complex distribution of retention versus loss for photosynthesis, plastid genomes, and plastid organelles. Reconstructing the evolution of all plastid and cytosolic metabolic pathways related to apicomplexan plastid function revealed an ancient dependency on plastid isoprenoid biosynthesis, predating the divergence of apicomplexan and dinoflagellates. Similarly, plastid genome retention is strongly linked to the retention of two genes in the plastid genome, sufB and clpC, altogether suggesting a relatively simple model for plastid retention and loss. Lastly, we examine the broader distribution of a suite of molecular characteristics previously linked to the origins of apicomplexan parasitism and find that virtually all are present in their free-living relatives. The emergence of parasitism may not be driven by acquisition of novel components, but rather by loss and modification of the existing, conserved traits.
PMID: 25717057 [PubMed – as supplied by publisher]
Feb 26
Metagenomic characterisation of viral communities in corals: Mining biological signal from methodological noise.
Metagenomic characterisation of viral communities in corals: Mining biological signal from methodological noise.
Environ Microbiol. 2015 Feb 24;
Authors: Wood-Charlson EM, Weynberg KD, Suttle CA, Roux S, van Oppen…
Feb 20
Whole-genome scans provide evidence of adaptive evolution in Malawian Plasmodium falciparum isolates.
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Whole-genome scans provide evidence of adaptive evolution in Malawian Plasmodium falciparum isolates.
J Infect Dis. 2014 Dec 15;210(12):1991-2000
Authors: Ocholla H, Preston MD, Mipando M, Jensen AT, Campino S, MacInnis B, Alcock D, Terlouw A, Zongo I, Oudraogo JB, Djimde AA, Assefa S, Doumbo OK, Borrmann S, Nzila A, Marsh K, Fairhurst RM, Nosten F, Anderson TJ, Kwiatkowski DP, Craig A, Clark TG, Montgomery J
Abstract
BACKGROUND: Selection by host immunity and antimalarial drugs has driven extensive adaptive evolution in Plasmodium falciparum and continues to produce ever-changing landscapes of genetic variation.
METHODS: We performed whole-genome sequencing of 69 P. falciparum isolates from Malawi and used population genetics approaches to investigate genetic diversity and population structure and identify loci under selection.
RESULTS: High genetic diversity (π = 2.4 × 10(-4)), moderately high multiplicity of infection (2.7), and low linkage disequilibrium (500-bp) were observed in Chikhwawa District, Malawi, an area of high malaria transmission. Allele frequency-based tests provided evidence of recent population growth in Malawi and detected potential targets of host immunity and candidate vaccine antigens. Comparison of the sequence variation between isolates from Malawi and those from 5 geographically dispersed countries (Kenya, Burkina Faso, Mali, Cambodia, and Thailand) detected population genetic differences between Africa and Asia, within Southeast Asia, and within Africa. Haplotype-based tests of selection to sequence data from all 6 populations identified signals of directional selection at known drug-resistance loci, including pfcrt, pfdhps, pfmdr1, and pfgch1.
CONCLUSIONS: The sequence variations observed at drug-resistance loci reflect differences in each country’s historical use of antimalarial drugs and may be useful in formulating local malaria treatment guidelines.
PMID: 24948693 [PubMed – indexed for MEDLINE]
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