January 2013 archive

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Study of cnidarian-algal symbiosis in the “omics” age.
Biol Bull. 2012 Aug;223(1):44-65
Authors: Meyer E, Weis VM
Abstract
The symbiotic associations between cnidarians and dinoflagellate alg…

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Dinoflagellate tandem array gene transcripts are highly conserved and not polycistronic.
Proc Natl Acad Sci U S A. 2012 Sep 25;109(39):15793-8
Authors: Beauchemin M, Roy S, Daoust P, Dagenais-Bellefeuille S,…

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Establishment of a Bacterial Expression System and Immunoassay Platform for the Major Capsid Protein of HcRNAV, a Dinoflagellate-Infecting RNA Virus.
Microbes Environ. 2012 Dec 7;27(4):483-9
Authors: Wada K,…

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ANALYSIS OF ALEXANDRIUM TAMARENSE (DINOPHYCEAE) GENES REVEALS THE COMPLEX EVOLUTIONARY HISTORY OF A MICROBIAL EUKARYOTE().
J Phycol. 2012 Oct 1;48(5):1130-1142
Authors: Chan CX, Soares MB, Bonaldo MF, Wisecav…

Counterion-mediated decompaction of liquid crystalline chromosomes.

DNA Cell Biol. 2012 Dec;31(12):1657-64

Authors: Sun S, Wong JT, Liu M, Dong F

Abstract
Liquid crystalline phases of DNA and nucleosome core particles can be formed in vitro, indicating the crucial roles of these phases in the maintenance and compaction of genomes in vivo. In the present study, sequential levels of liquid crystalline decompaction were identified in highly purified nuclei of Karenia papilionacea in response to the gradual chelation of divalent counterions by ethylenediaminetetraacetic acid (EDTA); the decompaction was observed using polarizing light microscopy, confocal laser scanning microscopy, and transmission electron microscopy and further confirmed utilizing microcalorimetry. Nested fibrous coils in 150 nm arc-like bands of chromatin were observed in the early stages of chromosomal decompaction. The microcalorimetry spectra of isolated nuclei revealed that the dynamic processes of nuclear decompaction occurred in a nonlinear manner; in addition, an EDTA-sensitive thermal transition between 60°C-70°C, corresponding to a liquid-crystalline-phase transition of chromosomes, was found. The results suggested that nested coils of fibrous chromatin filaments are responsible for the establishment and stabilization of the liquid crystalline and birefringence features of the chromosomes of dinoflagellates. The results also indicated that positively charged divalent counterions play significant roles in modulating liquid crystalline phases to compact the chromosomes of dinoflagellates.

PMID: 23072628 [PubMed – in process]

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Loss of nucleosomal DNA condensation coincides with appearance of a novel nuclear protein in dinoflagellates.

Curr Biol. 2012 Dec 18;22(24):2303-12

Authors: Gornik SG, Ford KL, Mulhern TD, Bacic A, McFadden GI, Waller RF

Abstract
BACKGROUND: The packaging, expression, and maintenance of nuclear genomes using histone proteins is a ubiquitous and fundamental feature of eukaryotic cells, yet the phylum Dinoflagellata has apparently abandoned this model of nuclear organization. Their nuclei contain permanently condensed, liquid crystalline chromosomes that seemingly lack histone proteins, and contain remarkably large genomes. The molecular basis for this reorganization is poorly understood, as is the sequence of evolutionary events that led to such radical change. We have investigated nuclear organization in the closest relative to dinoflagellates, Perkinsus marinus, and an early-branching dinoflagellate, Hematodinium sp., to identify early changes that occurred during dinoflagellate nuclear evolution.
RESULTS: We show that P. marinus has a typical nuclear organization that is based on the four core histones. By the early divergence of Hematodinium sp., however, dinoflagellate genome size is dramatically enlarged, chromosomes are permanently condensed, and histones are scarcely detectable. In place of histones, we identify a novel, dominant family of nuclear proteins that is only found in dinoflagellates and, surprisingly, in a family of large algal viruses, the Phycodnaviridae. These new proteins, which we call DVNPs (dinoflagellate/viral nucleoproteins), are highly basic, bind DNA with similar affinity to histones, and occur in multiple posttranslationally modified forms. We find these proteins throughout all dinoflagellates, including early- and late-branching taxa, but not in P. marinus.
CONCLUSIONS: Gain of a major novel family of nucleoproteins, apparently from an algal virus, occurred early in dinoflagellate evolution and coincides with rapid and dramatic reorganization of the dinoflagellate nucleus.

PMID: 23159597 [PubMed – in process]

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A Tertiary Plastid Gains RNA Editing in Its New Host.
Mol Biol Evol. 2012 Dec 17;
Authors: Jackson CJ, Gornik SG, Waller RF
Abstract
Dinoflagellates are known for their development of highly a…

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Molecular detection and species identification of Alexandrium (Dinophyceae) causing harmful algal blooms along the Chilean coastline.

AoB Plants. 2012;2012:pls033

Authors: Jedlicki A, Fernández G, Astorga M, Oyarzún P, Toro JE, Navarro JM, Martínez V

Abstract
BACKGROUND AND AIMS: On the basis of morphological evidence, the species involved in South American Pacific coast harmful algal blooms (HABs) has been traditionally recognized as Alexandrium catenella (Dinophyceae). However, these observations have not been confirmed using evidence based on genomic sequence variability. Our principal objective was to accurately determine the species of Alexandrium involved in local HABs in order to implement a real-time polymerase chain reaction (PCR) assay for its rapid and easy detection on filter-feeding shellfish, such as mussels.
METHODOLOGY: For species-specific determination, the intergenic spacer 1 (ITS1), 5.8S subunit, ITS2 and the hypervariable genomic regions D1-D5 of the large ribosomal subunit of local strains were sequenced and compared with two data sets of other Alexandrium sequences. Species-specific primers were used to amplify signature sequences within the genomic DNA of the studied species by conventional and real-time PCR.
PRINCIPAL RESULTS: Phylogenetic analysis determined that the Chilean strain falls into Group I of the tamarensis complex. Our results support the allocation of the Chilean Alexandrium species as a toxic Alexandrium tamarense rather than A. catenella, as currently defined. Once local species were determined to belong to Group I of the tamarensis complex, a highly sensitive and accurate real-time PCR procedure was developed to detect dinoflagellate presence in Mytilus spp. (Bivalvia) samples after being fed (challenged) in vitro with the Chilean Alexandrium strain. The results show that real-time PCR is useful to detect Alexandrium intake in filter-feeding molluscs.
CONCLUSIONS: It has been shown that the classification of local Alexandrium using morphological evidence is not very accurate. Molecular methods enabled the HAB dinoflagellate species of the Chilean coast to be assigned as A. tamarense rather than A. catenella. Real-time PCR analysis based on A. tamarense primers allowed the detection of dinoflagellate DNA in Mytilus spp. samples exposed to this alga. Through the specific assignment of dinoflagellate species involved in HABs, more reliable preventive policies can be implemented.

PMID: 23259043 [PubMed]