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Authors: Widmer G, Lee Y, Hunt P, Martinelli A, Tolkoff M, Bodi K
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Category: Uncategorized
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Comparative genome analysis of two Cryptosporidium parvum isolates with different host range.
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Evidence of purifying selection on merozoite surface protein 8 (MSP8) and 10 (MSP10) in Plasmodium spp.
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Nat Genet. 2012 Sep;44(9):1051-5
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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]
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An evolutionary perspective on the kinome of malaria parasites.
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Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals.
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Polyuridylylation and processing of transcripts from multiple gene minicircles in chloroplasts of the dinoflagellate Amphidinium carterae.
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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.
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Evolution of saxitoxin synthesis in cyanobacteria and dinoflagellates.
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Genome fragmentation is not confined to the peridinin plastid in dinoflagellates.
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PLoS One. 2012;7(6):e38809
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