Category Archive: Uncategorized

Dec 16

Genetic diversity of avian haemosporidians in Malaysia: cytochrome b lineages of the genera Plasmodium and Haemoproteus (Haemosporida) from Selangor.

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Genetic diversity of avian haemosporidians in Malaysia: cytochrome b lineages of the genera Plasmodium and Haemoproteus (Haemosporida) from Selangor.
Infect Genet Evol. 2015 Apr;31:33-9
Authors: Iv…

Dec 16

Molecular detection and genetic diversity of Babesia gibsoni in dogs in Bangladesh.

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Molecular detection and genetic diversity of Babesia gibsoni in dogs in Bangladesh.

Infect Genet Evol. 2015 Apr;31:53-60

Authors: Terao M, Akter S, Yasin MG, Nakao R, Kato H, Alam MZ, Katakura K

Abstract
Babesia gibsoni is a tick-borne hemoprotozoan parasite of dogs that often causes fever and hemolytic illness. Detection of B. gibsoni has been predominantly reported in Asian countries, including Japan, Korea, Taiwan, Malaysia, Bangladesh and India. The present study shows the first molecular characterization of B. gibsoni detected from dogs in Bangladesh. Blood samples were collected on FTA® Elute cards from 50 stray dogs in Mymensingh District in Bangladesh. DNA eluted from the cards was subjected to nested PCR for the 18S rRNA gene of Babesia species. Approximately 800bp PCR products were detected in 15 of 50 dogs (30%). Based on restriction fragment length polymorphism (RFLP) and direct sequencing of the PCR products, all parasite isolates were identified as B. gibsoni. Furthermore, the BgTRAP (B. gibsoni thrombospondin-related adhesive protein) gene fragments were detected in 13 of 15 18S rRNA gene PCR positive blood samples. Phylogenetic analysis of the BgTRAP gene revealed that B. gibsoni parasites in Bangladesh formed a cluster, which was genetically different from other Asian B. gibsoni isolates. In addition, tandem repeat analysis of the BgTRAP gene clearly showed considerable genetic variation among Bangladeshi isolates. These results suggested that B. gibsoni parasites in a different genetic clade are endemic in dogs in Bangladesh. Further studies are required to elucidate the origin, distribution, vector and pathogenesis of B. gibsoni parasites circulating in dogs in Bangladesh.

PMID: 25620376 [PubMed – indexed for MEDLINE]

Dec 10

Diversity and Divergence of Dinofagellate Histone Proteins.

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Diversity and Divergence of Dinofagellate Histone Proteins.

G3 (Bethesda). 2015 Dec 8;

Authors: Marinov GK, Lynch M

Abstract
Histone proteins and the nucleosomal organization of chromatin are near-universal eukaroytic features, with the exception of dinoflagellates. Previous studies have suggested that histones do not play a major role in the packaging of dinoflagellate genomes, although several genomic and transcriptomic surveys have detected a full set of core histone genes. Here, transcriptomic and genomic sequence data from multiple dinoflagellate lineages are analyzed, and the diversity of histone proteins and their variants characterized, with particular focus on their potential posttranslational modifications and the conservation of the histone code. In addition, the set of putative epigenetic mark readers and writers, chromatin remodelers and histone chaperones are examined. Dinoflagellates clearly express the most derived set of histones among all autonomous eukaryote nuclei, consistent with a combination of relaxation of sequence con-straints imposed by the histone code and the presence of numerous specialized histone variants. The histone code itself appears to have diverged significantly in some of its compo-nents, yet others are conserved, implying conservation of the associated biochemical processes. Specifically, and with major implications for the function of histones in dinoflagellates, the results presented here strongly suggest that transcription through nucleosomal arrays happens in dinoflagellates. Finally, the plausible roles of histones in dinoflagellate nuclei are discussed.

PMID: 26646152 [PubMed – as supplied by publisher]

Dec 09

Biosynthetic Studies of 13-Desmethylspirolide C Produced by Alexandrium ostenfeldii (= A. peruvianum): Rationalization of the Biosynthetic Pathway Following Incorporation of (13)C-Labeled Methionine and Application of the Odd-Even Rule of Methylation.

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Biosynthetic Studies of 13-Desmethylspirolide C Produced by Alexandrium ostenfeldii (= A. peruvianum): Rationalization of the Biosynthetic Pathway Following Incorporation of (13)C-Labeled Methionine and Application of the Odd…

Dec 03

Gene Loss and Error-Prone RNA Editing in the Mitochondrion of Perkinsela, an Endosymbiotic Kinetoplastid.

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Gene Loss and Error-Prone RNA Editing in the Mitochondrion of Perkinsela, an Endosymbiotic Kinetoplastid.

MBio. 2015;6(6)

Authors: David V, Flegontov P, Gerasimov E, Tanifuji G, Hashimi H, Logacheva MD, Maruyama S, Onodera NT, Gray MW, Archibald JM, Lukeš J

Abstract
UNLABELLED: Perkinsela is an enigmatic early-branching kinetoplastid protist that lives as an obligate endosymbiont inside Paramoeba (Amoebozoa). We have sequenced the highly reduced mitochondrial genome of Perkinsela, which possesses only six protein-coding genes (cox1, cox2, cox3, cob, atp6, and rps12), despite the fact that the organelle itself contains more DNA than is present in either the host or endosymbiont nuclear genomes. An in silico analysis of two Perkinsela strains showed that mitochondrial RNA editing and processing machineries typical of kinetoplastid flagellates are generally conserved, and all mitochondrial transcripts undergo U-insertion/deletion editing. Canonical kinetoplastid mitochondrial ribosomes are also present. We have developed software tools for accurate and exhaustive mapping of transcriptome sequencing (RNA-seq) reads with extensive U-insertions/deletions, which allows detailed investigation of RNA editing via deep sequencing. With these methods, we show that up to 50% of reads for a given edited region contain errors of the editing system or, less likely, correspond to alternatively edited transcripts.
IMPORTANCE: Uridine insertion/deletion-type RNA editing, which occurs in the mitochondrion of kinetoplastid protists, has been well-studied in the model parasite genera Trypanosoma, Leishmania, and Crithidia. Perkinsela provides a unique opportunity to broaden our knowledge of RNA editing machinery from an evolutionary perspective, as it represents the earliest kinetoplastid branch and is an obligatory endosymbiont with extensive reductive trends. Interestingly, up to 50% of mitochondrial transcripts in Perkinsela contain errors. Our study was complemented by use of newly developed software designed for accurate mapping of extensively edited RNA-seq reads obtained by deep sequencing.

PMID: 26628723 [PubMed – in process]

Nov 25

The Hidden Sexuality of Alexandrium Minutum: An Example of Overlooked Sex in Dinoflagellates.

The Hidden Sexuality of Alexandrium Minutum: An Example of Overlooked Sex in Dinoflagellates.
PLoS One. 2015;10(11):e0142667
Authors: Figueroa RI, Dapena C, Bravo I, Cuadrado A
Abstract
Dinoflagella…

Nov 18

Multifunctional polyketide synthase genes identified by genomic survey of the symbiotic dinoflagellate, Symbiodinium minutum.

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Multifunctional polyketide synthase genes identified by genomic survey of the symbiotic dinoflagellate, Symbiodinium minutum.
BMC Genomics. 2015;16(1):941
Authors: Beedessee G, Hisata K, Roy MC, Sat…

Nov 13

RNA Sequencing Revealed Numerous Polyketide Synthase Genes in the Harmful Dinoflagellate Karenia mikimotoi.

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RNA Sequencing Revealed Numerous Polyketide Synthase Genes in the Harmful Dinoflagellate Karenia mikimotoi.
PLoS One. 2015;10(11):e0142731
Authors: Kimura K, Okuda S, Nakayama K, Shikata T, Takahash…

Nov 07

The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and coral symbiosis.

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The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and coral symbiosis.
Science. 2015 Nov 6;350(6261):691-4
Authors: Lin S, Cheng S, Song B, Zhong X, Lin X, Li W, Li L, Zha…

Oct 29

A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains.

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A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains.

Nat Commun. 2014;5:4052

Authors: Preston MD, Campino S, Assefa SA, Echeverry DF, Ocholla H, Amambua-Ngwa A, Stewart LB, Conway DJ, Borrmann S, Michon P, Zongo I, Ouédraogo JB, Djimde AA, Doumbo OK, Nosten F, Pain A, Bousema T, Drakeley CJ, Fairhurst RM, Sutherland CJ, Roper C, Clark TG

Abstract
Malaria is a major public health problem that is actively being addressed in a global eradication campaign. Increased population mobility through international air travel has elevated the risk of re-introducing parasites to elimination areas and dispersing drug-resistant parasites to new regions. A simple genetic marker that quickly and accurately identifies the geographic origin of infections would be a valuable public health tool for locating the source of imported outbreaks. Here we analyse the mitochondrion and apicoplast genomes of 711 Plasmodium falciparum isolates from 14 countries, and find evidence that they are non-recombining and co-inherited. The high degree of linkage produces a panel of relatively few single-nucleotide polymorphisms (SNPs) that is geographically informative. We design a 23-SNP barcode that is highly predictive (~92%) and easily adapted to aid case management in the field and survey parasite migration worldwide.

PMID: 24923250 [PubMed – indexed for MEDLINE]

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