Claudio Slamovits
Author's posts
Jan 21
Admixture and recombination among Toxoplasma gondii lineages explain global genome diversity.
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Admixture and recombination among Toxoplasma gondii lineages explain global genome diversity.
Proc Natl Acad Sci U S A. 2012 Aug 14;109(33):13458-63
Authors: Minot S, Melo MB, Li F, Lu D, Niedelman W, Levine SS, Saeij JP
Abstract
Toxoplasma gondii is a highly successful protozoan parasite that infects all warm-blooded animals and causes severe disease in immunocompromised and immune-naïve humans. It has an unusual global population structure: In North America and Europe, isolated strains fall predominantly into four largely clonal lineages, but in South America there is great genetic diversity and the North American clonal lineages are rarely found. Genetic variation between Toxoplasma strains determines differences in virulence, modulation of host-signaling pathways, growth, dissemination, and disease severity in mice and likely in humans. Most studies on Toxoplasma genetic variation have focused on either a few loci in many strains or low-resolution genome analysis of three clonal lineages. We use whole-genome sequencing to identify a large number of SNPs between 10 Toxoplasma strains from Europe and North and South America. These were used to identify haplotype blocks (genomic regions) shared between strains and construct a Toxoplasma haplotype map. Additional SNP analysis of RNA-sequencing data of 26 Toxoplasma strains, representing global diversity, allowed us to construct a comprehensive genealogy for Toxoplasma gondii that incorporates sexual recombination. These data show that most current isolates are recent recombinants and cannot be easily grouped into a limited number of haplogroups. A complex picture emerges in which some genomic regions have not been recently exchanged between any strains, and others recently spread from one strain to many others.
PMID: 22847430 [PubMed – indexed for MEDLINE]
Jan 21
Plasmodium cynomolgi genome sequences provide insight into Plasmodium vivax and the monkey malaria clade.
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Plasmodium cynomolgi genome sequences provide insight into Plasmodium vivax and the monkey malaria clade.
Nat Genet. 2012 Sep;44(9):1051-5
Authors: Tachibana S, Sullivan SA, Kawai S, Nakamura S, Kim HR, Goto…
Jan 21
An evolutionary perspective on the kinome of malaria parasites.
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An evolutionary perspective on the kinome of malaria parasites.
Philos Trans R Soc Lond B Biol Sci. 2012 Sep 19;367(1602):2607-18
Authors: Talevich E, Tobin AB, Kannan N, Doerig C
Abstract
Ma…
Jan 21
Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals.
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Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals.
PLoS One. 2012;7(4):e35269
Authors: Bayer T, Aranda M, Sunagawa S, Yum LK, Desalvo MK, Lindquist E, Co…
Jan 21
Structure of metaphase chromosomes: a role for effects of macromolecular crowding.
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Structure of metaphase chromosomes: a role for effects of macromolecular crowding.
PLoS One. 2012;7(4):e36045
Authors: Hancock R
Abstract
In metaphase chromosomes, chromatin is compacted to a concentration of several hundred mg/ml by mechanisms which remain elusive. Effects mediated by the ionic environment are considered most frequently because mono- and di-valent cations cause polynucleosome chains to form compact ~30-nm diameter fibres in vitro, but this conformation is not detected in chromosomes in situ. A further unconsidered factor is predicted to influence the compaction of chromosomes, namely the forces which arise from crowding by macromolecules in the surrounding cytoplasm whose measured concentration is 100-200 mg/ml. To mimic these conditions, chromosomes were released from mitotic CHO cells in solutions containing an inert volume-occupying macromolecule (8 kDa polyethylene glycol, 10.5 kDa dextran, or 70 kDa Ficoll) in 100 µM K-Hepes buffer, with contaminating cations at only low micromolar concentrations. Optical and electron microscopy showed that these chromosomes conserved their characteristic structure and compaction, and their volume varied inversely with the concentration of a crowding macromolecule. They showed a canonical nucleosomal structure and contained the characteristic proteins topoisomerase IIα and the condensin subunit SMC2. These observations, together with evidence that the cytoplasm is crowded in vivo, suggest that macromolecular crowding effects should be considered a significant and perhaps major factor in compacting chromosomes. This model may explain why ~30-nm fibres characteristic of cation-mediated compaction are not seen in chromosomes in situ. Considering that crowding by cytoplasmic macromolecules maintains the compaction of bacterial chromosomes and has been proposed to form the liquid crystalline chromosomes of dinoflagellates, a crowded environment may be an essential characteristic of all genomes.
PMID: 22540018 [PubMed – indexed for MEDLINE]
Jan 21
Polyuridylylation and processing of transcripts from multiple gene minicircles in chloroplasts of the dinoflagellate Amphidinium carterae.
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Polyuridylylation and processing of transcripts from multiple gene minicircles in chloroplasts of the dinoflagellate Amphidinium carterae.
Plant Mol Biol. 2012 Jul;79(4-5):347-57
Authors: Barbrook AC, Dorrel…
Jan 21
Evolution of saxitoxin synthesis in cyanobacteria and dinoflagellates.
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Evolution of saxitoxin synthesis in cyanobacteria and dinoflagellates.
Mol Biol Evol. 2013 Jan;30(1):70-8
Authors: Hackett JD, Wisecaver JH, Brosnahan ML, Kulis DM, Anderson DM, Bhattacharya D, Plumley FG, E…
Jan 21
Radiolaria associated with large diversity of marine alveolates.
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Radiolaria associated with large diversity of marine alveolates.
Protist. 2012 Sep;163(5):767-77
Authors: Bråte J, Krabberød AK, Dolven JK, Ose RF, Kristensen T, Bjørklund KR, Shalchian-Tabrizi K
Abstract
We have isolated cells of unculturable radiolarians from marine coastal waters. Individual cells were subjected to single cell whole genome amplification (SCWGA) and gene-targeted PCR. Using this approach we recover a surprisingly large diversity of sequences related to the enigmatic marine alveolate groups 1 and 2 (MALV I and MALV II) that most likely represent intracellular symbionts or parasites of the radiolarian cells. 18S rDNA phylogeny of the MALV sequences reveals 4 distinct clades of radiolarian associates here named Radiolarian Associated Sequences (RAS) 1-4. One clade of both phaeodarian and radiolarian associates and one clade of only phaeodarian associates are also identified. The MALV sequences cluster according to host type, i.e. sequences from associates identified in radiolarians, fish, copepods, ciliates or dinoflagellates are not intermixed but separated into distinct clades. This implies several independent colonizations of host lineages and links a large diversity of MALV to radiolarian-associated species. This demonstrates that radiolarians may be an important reservoir for MALV, making them a key group for understanding the impact of intracellular symbionts on the marine ecosystem. This study shows that applying SCWGA on unculturable cells is a promising approach to study the vast diversity and interactions of intracellular eukaryote organisms.
PMID: 22658831 [PubMed – indexed for MEDLINE]
Jan 21
Genome fragmentation is not confined to the peridinin plastid in dinoflagellates.
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Genome fragmentation is not confined to the peridinin plastid in dinoflagellates.
PLoS One. 2012;7(6):e38809
Authors: Espelund M, Minge MA, Gabrielsen TM, Nederbragt AJ, Shalchian-Tabrizi K, Otis C, Turmel …
Jan 21
Developing the anemone Aiptasia as a tractable model for cnidarian-dinoflagellate symbiosis: the transcriptome of aposymbiotic A. pallida.
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Developing the anemone Aiptasia as a tractable model for cnidarian-dinoflagellate symbiosis: the transcriptome of aposymbiotic A. pallida.
BMC Genomics. 2012;13:271
Authors: Lehnert EM, Burriesci MS, Pringl…