Slamovits Lab at Dalhousie University

Category: Uncategorized

  • 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]

  • 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 some of the most diverse and productive ecosystems on the planet, but are threatened by global and local stressors, mandating the need for incorporating ex situ conservation practices. One approach that is highly protective is the development of genome resource banks that preserve the species and its genetic diversity. A critical component of the reef are the endosymbiotic algae, Symbiodinium sp., living within most coral that transfer energy-rich sugars to their hosts. Although Symbiodinium are maintained alive in culture collections around the world, the cryopreservation of these algae to prevent loss and genetic drift is not well-defined. This study examined the quantum yield physiology and freezing protocols that resulted in survival of Symbiodinium at 24 h post-thawing. Only the ultra-rapid procedure called vitrification resulted in success whereas conventional slow freezing protocols did not. We determined that success also depended on using a thin film of agar with embedded Symbiodinium on Cryotops, a process that yielded a post-thaw viability of >50% in extracted and vitrified Symbiodinium from Fungia scutaria, Pocillopora damicornis and Porites compressa. Additionally, there also was a seasonal influence on vitrification success as the best post-thaw survival of F. scutaria occurred in winter and spring compared to summer and fall (P < 0.05). These findings lay the foundation for developing a viable genome resource bank for the world’s Symbiodinium that, in turn, will not only protect this critical element of coral functionality but serve as a resource for understanding the complexities of symbiosis, support selective breeding experiments to develop more thermally resilient strains of coral, and provide a ‘gold-standard’ genomics collection, allowing for full genomic sequencing of unique Symbiodinium strains.

    PMID: 26422237 [PubMed – as supplied by publisher]

  • 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 context-aware self-organizing systems. One of its emerging properties is a modular architecture. Such modular architecture has been identified as domains and defined as its units of evolution and function. However, this modular architecture is not exclusively defined by domains. Also, the definition of a domain is an ongoing debate. Here we propose differentiating structural, evolutionary and functional domains as distinct concepts. Defining domains or modules is confounded by diverse definitions of the concept, and also by other elements inherent to protein structures. An apparent hierarchy in protein structure architecture is one of these elements, where lower level interactions may create noise for the definition of higher levels. Diverse modularity-molding factors such as folding, function, and selection, can have a misleading effect when trying to define a given type of module. It is thus important to keep in mind this complexity when defining modularity in protein structures and interpreting the outcome modularity inference approaches.

    PMID: 26412786 [PubMed – as supplied by publisher]

  • Identification of microRNAs in the Toxigenic Dinoflagellate Alexandrium catenella by High-Throughput Illumina Sequencing and Bioinformatic Analysis.

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    Identification of microRNAs in the Toxigenic Dinoflagellate Alexandrium catenella by High-Throughput Illumina Sequencing and Bioinformatic Analysis.

    PLoS One. 2015;10(9):e0138709

    Authors: Geng H, Sui Z, Zhang S, Du Q, Ren Y, Liu Y, Kong F, Zhong J, Ma Q

    Abstract
    Micro-ribonucleic acids (miRNAs) are a large group of endogenous, tiny, non-coding RNAs consisting of 19-25 nucleotides that regulate gene expression at either the transcriptional or post-transcriptional level by mediating gene silencing in eukaryotes. They are considered to be important regulators that affect growth, development, and response to various stresses in plants. Alexandrium catenella is an important marine toxic phytoplankton species that can cause harmful algal blooms (HABs). To date, identification and function analysis of miRNAs in A. catenella remain largely unexamined. In this study, high-throughput sequencing was performed on A. catenella to identify and quantitatively profile the repertoire of small RNAs from two different growth phases. A total of 38,092,056 and 32,969,156 raw reads were obtained from the two small RNA libraries, respectively. In total, 88 mature miRNAs belonging to 32 miRNA families were identified. Significant differences were found in the member number, expression level of various families, and expression abundance of each member within a family. A total of 15 potentially novel miRNAs were identified. Comparative profiling showed that 12 known miRNAs exhibited differential expression between the lag phase and the logarithmic phase. Real-time quantitative RT-PCR (qPCR) was performed to confirm the expression of two differentially expressed miRNAs that were one up-regulated novel miRNA (aca-miR-3p-456915), and one down-regulated conserved miRNA (tae-miR159a). The expression trend of the qPCR assay was generally consistent with the deep sequencing result. Target predictions of the 12 differentially expressed miRNAs resulted in 1813target genes. Gene ontology (GO) analysis and the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG) annotations revealed that some miRNAs were associated with growth and developmental processes of the alga. These results provide insights into the roles that miRNAs play in the growth of A. catenella, and they provide the basis for further studies of the molecular mechanisms that underlie bloom growth in red tides species.

    PMID: 26398216 [PubMed – as supplied by publisher]

  • Projection scenarios of body mass index (2013-2030) for Public Health Planning in Quebec.

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    Projection scenarios of body mass index (2013-2030) for Public Health Planning in Quebec.

    BMC Public Health. 2014;14:996

    Authors: Lo E, Hamel D, Jen Y, Lamontagne P, Martel S, Steensma C, Blouin C, Steele R

    Abstract
    BACKGROUND: Projection analyses can provide estimates of the future health burden of increasing BMI and represent a relevant and useful tool for public health planning. Our study presents long-term (2013-2030) projections of the prevalence and numbers of individuals by BMI category for adult men and women in Quebec. Three applications of projections to estimate outcomes more directly pertinent to public health planning, as well as an in-depth discussion of limits, are provided with the aim of encouraging greater use of projection analyses by public health officers.
    METHODS: The weighted compositional regression method is applied to prevalence time series derived from sixteen cross-sectional survey cycles, for scenarios of linear change and deceleration. Estimation of the component of projected change potentially amenable to intervention, future health targets and the projected impact on type 2 diabetes, were done.
    RESULTS: Obesity prevalence in Quebec is projected to rise steadily from 2013 to 2030 in both men (from 18.0-19.4% to 22.2-30.4%) and women (from 15.5-16.3% to 18.2-22.4%). Corresponding projected numbers of obese individuals are (579,000-625,000 to 790,000-1,084,000) in men and (514,000-543,000 to 661,000-816,000) in women. These projected increases are found to be primarily an ‘epidemiologic’ rather than ‘demographic’ phenomenon and thus potentially amenable to public health intervention. Assessment of obesity targets for 2020 illustrates the necessity of using projected rather than current prevalence; for example a targeted 2% drop in obesity prevalence relative to 2013 translates into a 3.6-5.4% drop relative to 2020 projected levels. Type 2 diabetes is projected to increase from 6.9% to 9.2-10.1% in men and from 5.7% to 7.1-7.5% in women, from 2011-2012 to 2030. A substantial proportion of this change (25-44% for men, and 27-43% for women) is attributable to the changing BMI distribution.
    CONCLUSIONS: Obesity in Quebec is projected to increase and should therefore continue to be a public health priority. Application of projections to estimate the proportion of change potentially amenable to intervention, feasible health targets, and future chronic disease prevalence are demonstrated. Projection analyses have limitations, but represent a pertinent tool for public health planning.

    PMID: 25253196 [PubMed – indexed for MEDLINE]

  • Phylogenomics Reveals Convergent Evolution of Lifestyles in Close Relatives of Animals and Fungi.

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    Phylogenomics Reveals Convergent Evolution of Lifestyles in Close Relatives of Animals and Fungi.

    Curr Biol. 2015 Sep 9;

    Authors: Torruella G, de Mendoza A, Grau-Bové X, Antó M, Chaplin MA, Del Campo J, Eme L, Pérez-Cordón G, Whipps CM, Nichols KM, Paley R, Roger AJ, Sitjà-Bobadilla A, Donachie S, Ruiz-Trillo I

    Abstract
    The Opisthokonta are a eukaryotic supergroup divided in two main lineages: animals and related protistan taxa, and fungi and their allies [1, 2]. There is a great diversity of lifestyles and morphologies among unicellular opisthokonts, from free-living phagotrophic flagellated bacterivores and filopodiated amoebas to cell-walled osmotrophic parasites and saprotrophs. However, these characteristics do not group into monophyletic assemblages, suggesting rampant convergent evolution within Opisthokonta. To test this hypothesis, we assembled a new phylogenomic dataset via sequencing 12 new strains of protists. Phylogenetic relationships among opisthokonts revealed independent origins of filopodiated amoebas in two lineages, one related to fungi and the other to animals. Moreover, we observed that specialized osmotrophic lifestyles evolved independently in fungi and protistan relatives of animals, indicating convergent evolution. We therefore analyzed the evolution of two key fungal characters in Opisthokonta, the flagellum and chitin synthases. Comparative analyses of the flagellar toolkit showed a previously unnoticed flagellar apparatus in two close relatives of animals, the filasterean Ministeria vibrans and Corallochytrium limacisporum. This implies that at least four different opisthokont lineages secondarily underwent flagellar simplification. Analysis of the evolutionary history of chitin synthases revealed significant expansions in both animals and fungi, and also in the Ichthyosporea and C. limacisporum, a group of cell-walled animal relatives. This indicates that the last opisthokont common ancestor had a complex toolkit of chitin synthases that was differentially retained in extant lineages. Thus, our data provide evidence for convergent evolution of specialized lifestyles in close relatives of animals and fungi from a generalist ancestor.

    PMID: 26365255 [PubMed – as supplied by publisher]

  • The genome of Aiptasia, a sea anemone model for coral symbiosis.

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    The genome of Aiptasia, a sea anemone model for coral symbiosis.

    Proc Natl Acad Sci U S A. 2015 Aug 31;

    Authors: Baumgarten S, Simakov O, Esherick LY, Liew YJ, Lehnert EM, Michell CT, Li Y, Hambleton EA, Guse A, Oates ME, Gough J, Weis VM, Aranda M, Pringle JR, Voolstra CR

    Abstract
    The most diverse marine ecosystems, coral reefs, depend upon a functional symbiosis between a cnidarian animal host (the coral) and intracellular photosynthetic dinoflagellate algae. The molecular and cellular mechanisms underlying this endosymbiosis are not well understood, in part because of the difficulties of experimental work with corals. The small sea anemone Aiptasia provides a tractable laboratory model for investigating these mechanisms. Here we report on the assembly and analysis of the Aiptasia genome, which will provide a foundation for future studies and has revealed several features that may be key to understanding the evolution and function of the endosymbiosis. These features include genomic rearrangements and taxonomically restricted genes that may be functionally related to the symbiosis, aspects of host dependence on alga-derived nutrients, a novel and expanded cnidarian-specific family of putative pattern-recognition receptors that might be involved in the animal-algal interactions, and extensive lineage-specific horizontal gene transfer. Extensive integration of genes of prokaryotic origin, including genes for antimicrobial peptides, presumably reflects an intimate association of the animal-algal pair also with its prokaryotic microbiome.

    PMID: 26324906 [PubMed – as supplied by publisher]

  • Diversity and origins of anaerobic metabolism in mitochondria and related organelles.

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    Diversity and origins of anaerobic metabolism in mitochondria and related organelles.

    Philos Trans R Soc Lond B Biol Sci. 2015 Sep 26;370(1678)

    Authors: Stairs CW, Leger MM, Roger AJ

    Abstract
    Across the diversity of life, organisms have evolved different strategies to thrive in hypoxic environments, and microbial eukaryotes (protists) are no exception. Protists that experience hypoxia often possess metabolically distinct mitochondria called mitochondrion-related organelles (MROs). While there are some common metabolic features shared between the MROs of distantly related protists, these organelles have evolved independently multiple times across the breadth of eukaryotic diversity. Until recently, much of our knowledge regarding the metabolic potential of different MROs was limited to studies in parasitic lineages. Over the past decade, deep-sequencing studies of free-living anaerobic protists have revealed novel configurations of metabolic pathways that have been co-opted for life in low oxygen environments. Here, we provide recent examples of anaerobic metabolism in the MROs of free-living protists and their parasitic relatives. Additionally, we outline evolutionary scenarios to explain the origins of these anaerobic pathways in eukaryotes.

    PMID: 26323757 [PubMed – in process]

  • Eukaryotes first: how could that be?

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    Eukaryotes first: how could that be?

    Philos Trans R Soc Lond B Biol Sci. 2015 Sep 26;370(1678)

    Authors: Mariscal C, Doolittle WF

    Abstract
    In the half century since the formulation of the prokaryote : eukaryote dichotomy, many authors have proposed that the former evolved from something resembling the latter, in defiance of common (and possibly common sense) views. In such ‘eukaryotes first’ (EF) scenarios, the last universal common ancestor is imagined to have possessed significantly many of the complex characteristics of contemporary eukaryotes, as relics of an earlier ‘progenotic’ period or RNA world. Bacteria and Archaea thus must have lost these complex features secondarily, through ‘streamlining’. If the canonical three-domain tree in which Archaea and Eukarya are sisters is accepted, EF entails that Bacteria and Archaea are convergently prokaryotic. We ask what this means and how it might be tested.

    PMID: 26323754 [PubMed – in process]

  • Symbiosis becoming permanent: Survival of the luckiest.

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    Symbiosis becoming permanent: Survival of the luckiest.

    Proc Natl Acad Sci U S A. 2015 Aug 18;112(33):10101-3

    Authors: Keeling PJ, McCutcheon JP, Doolittle WF

    PMID: 26283342 [PubMed – in process]