Claudio Slamovits
Author's posts
Jan 21
Molecular detection and species identification of Alexandrium (Dinophyceae) causing harmful algal blooms along the Chilean coastline.
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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]
Jan 18
Mitochondrial evolution.
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Mitochondrial evolution.
Cold Spring Harb Perspect Biol. 2012 Sep;4(9):a011403
Authors: Gray MW
Abstract
Viewed through the lens of the genome it contains, the mitochondrion is of unquestioned bacterial ancestry, originating from within the bacterial phylum α-Proteobacteria (Alphaproteobacteria). Accordingly, the endosymbiont hypothesis–the idea that the mitochondrion evolved from a bacterial progenitor via symbiosis within an essentially eukaryotic host cell–has assumed the status of a theory. Yet mitochondrial genome evolution has taken radically different pathways in diverse eukaryotic lineages, and the organelle itself is increasingly viewed as a genetic and functional mosaic, with the bulk of the mitochondrial proteome having an evolutionary origin outside Alphaproteobacteria. New data continue to reshape our views regarding mitochondrial evolution, particularly raising the question of whether the mitochondrion originated after the eukaryotic cell arose, as assumed in the classical endosymbiont hypothesis, or whether this organelle had its beginning at the same time as the cell containing it.
PMID: 22952398 [PubMed – indexed for MEDLINE]
Jan 07
We support Bust-a-Move to get better breast cancer care for Nova Scotia
Bustamove Halifax is a fundraising effort by a partnership between the QEII, IWK and Capital Health to help build an integrated, world-class Breast Health Centre in Halifax where all the necessary equipment is available, patient services are coordinated, and resources and supports are accessible to all breast cancer patients and their families. Our postdoc Susana Breglia …
Jan 06
NAI and SMBE Satellite Workshop on the Origin of Life
21-24 January 2013Princeton University Center for Theoretical Science Organizers: Laura Landweber and Aaron Goldman http://www.pctp.princeton.edu/pcts/Originoflife2013/Originoflife2013.html The last few decades have witnessed the burgeoning of many highly productive lines of investigation into abiogenesis and the early emergence of biological complexity. Planetary sciences and geochemistry have produced a short-list of well-studied settings where prebiotic chemistry may have …
Jan 06
Rapid identification of high-confidence taxonomic assignments for metagenomic data.
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Rapid identification of high-confidence taxonomic assignments for metagenomic data.
Nucleic Acids Res. 2012 Aug;40(14):e111
Authors: MacDonald NJ, Parks DH, Beiko RG
Abstract
Determining the…
Jan 06
Aggregative multicellularity evolved independently in the eukaryotic supergroup Rhizaria.
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Aggregative multicellularity evolved independently in the eukaryotic supergroup Rhizaria.
Curr Biol. 2012 Jun 19;22(12):1123-7
Authors: Brown MW, Kolisko M, Silberman JD, Roger AJ
Abstract
Mu…
Jan 06
Evolutionary origin of RNA editing.
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Evolutionary origin of RNA editing.
Biochemistry. 2012 Jul 3;51(26):5235-42
Authors: Gray MW
Abstract
The term “RNA editing” encompasses a wide variety of mechanistically and phylogenetically…
Jan 06
Population genomics: how bacterial species form and why they don't exist.
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Population genomics: how bacterial species form and why they don’t exist.
Curr Biol. 2012 Jun 5;22(11):R451-3
Authors: Doolittle WF
Abstract
Two processes suggested to drive bacterial speciat…
Jan 06
Composition of the mitochondrial electron transport chain in acanthamoeba castellanii: structural and evolutionary insights.
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Composition of the mitochondrial electron transport chain in acanthamoeba castellanii: structural and evolutionary insights.
Biochim Biophys Acta. 2012 Nov;1817(11):2027-37
Authors: Gawryluk RM, Chisholm KA, Pinto DM, Gray MW
Abstract
The mitochondrion, derived in evolution from an α-proteobacterial progenitor, plays a key metabolic role in eukaryotes. Mitochondria house the electron transport chain (ETC) that couples oxidation of organic substrates and electron transfer to proton pumping and synthesis of ATP. The ETC comprises several multiprotein enzyme complexes, all of which have counterparts in bacteria. However, mitochondrial ETC assemblies from animals, plants and fungi are generally more complex than their bacterial counterparts, with a number of ‘supernumerary’ subunits appearing early in eukaryotic evolution. Little is known, however, about the ETC of unicellular eukaryotes (protists), which are key to understanding the evolution of mitochondria and the ETC. We present an analysis of the ETC proteome from Acanthamoeba castellanii, an ecologically, medically and evolutionarily important member of Amoebozoa (sister to Opisthokonta). Data obtained from tandem mass spectrometric (MS/MS) analyses of purified mitochondria as well as ETC complexes isolated via blue native polyacrylamide gel electrophoresis are combined with the results of bioinformatic queries of sequence databases. Our bioinformatic analyses have identified most of the ETC subunits found in other eukaryotes, confirming and extending previous observations. The assignment of proteins as ETC subunits by MS/MS provides important insights into the primary structures of ETC proteins and makes possible, through the use of sensitive profile-based similarity searches, the identification of novel constituents of the ETC along with the annotation of highly divergent but phylogenetically conserved ETC subunits.
PMID: 22709906 [PubMed – indexed for MEDLINE]
Jan 06
Absence of a universal element for tRNAHis identity in Acanthamoeba castellanii.
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Absence of a universal element for tRNAHis identity in Acanthamoeba castellanii.
Nucleic Acids Res. 2012 Dec 14;
Authors: Rao BS, Mohammad F, Gray MW, Jackman JE
Abstract
The additional G(-1) …