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Sep 01
Paralytic shellfish toxin biosynthesis in cyanobacteria and dinoflagellates: a molecular overview.
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Paralytic shellfish toxin biosynthesis in cyanobacteria and dinoflagellates: a molecular overview.
J Proteomics. 2015 Aug 24;
Authors: Wang DZ, Zhang SF, Zhang Y, Lin L
Abstract
Para…
Aug 16
NextGen sequencing reveals short double crossovers contribute disproportionately to genetic diversity in Toxoplasma gondii.
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NextGen sequencing reveals short double crossovers contribute disproportionately to genetic diversity in Toxoplasma gondii.
BMC Genomics. 2014;15:1168
Authors: Khan A, Shaik JS, Behnke M, Wang Q, …
Aug 16
Multilevel selection theory and the evolutionary functions of transposable elements.
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Multilevel selection theory and the evolutionary functions of transposable elements.
Genome Biol Evol. 2015 Aug 6;
Authors: Brunet TD, Doolittle WF
Abstract
One of several issues at …
Aug 07
Heterologous DNA Uptake in Cultured Symbiodinium spp. Aided by Agrobacterium tumefaciens.
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Heterologous DNA Uptake in Cultured Symbiodinium spp. Aided by Agrobacterium tumefaciens.
PLoS One. 2015;10(7):e0132693
Authors: Ortiz-Matamoros MF, Islas-Flores T, Voigt B, Menzel D, Baluška F, Villanueva MA
Abstract
Plant-targeted pCB302 plasmids containing sequences encoding gfp fusions with a microtubule-binding domain; gfp with the fimbrin actin-binding domain 2; and gfp with AtRACK1C from Arabidopsis thaliana, all harbored in Agrobacterium tumefaciens, were used to assay heterologous expression on three different clades of the photosynthetic dinoflagellate, Symbiodinium. Accessibility to the resistant cell wall and through the plasma membrane of these dinoflagellates was gained after brief but vigorous shaking in the presence of glass beads and polyethylene glycol. A resistance gene to the herbicide Basta allowed appropriate selection of the cells expressing the hybrid proteins, which showed a characteristic green fluorescence, although they appeared to lose their photosynthetic pigments and did not further divide. Cell GFP expression frequency measured as green fluorescence emission yielded 839 per every 106 cells for Symbiodinium kawagutii, followed by 640 and 460 per every 106 cells for Symbiodinium microadriaticum and Symbiodinium sp. Mf11, respectively. Genomic PCR with specific primers amplified the AtRACK1C and gfp sequences after selection in all clades, thus revealing their presence in the cells. RT-PCR from RNA of S. kawagutii co-incubated with A. tumefaciens harboring each of the three vectors with their respective constructs, amplified products corresponding to the heterologous gfp sequence while no products were obtained from three distinct negative controls. The reported procedure shows that mild abrasion followed by co-incubation with A. tumefaciens harboring heterologous plasmids with CaMV35S and nos promoters can lead to expression of the encoded proteins into the Symbiodinium cells in culture. Despite the obvious drawbacks of the procedure, this is an important first step towards a stable transformation of Symbiodinium.
PMID: 26167858 [PubMed – in process]
Aug 07
Single-cell transcriptomics using spliced leader PCR: Evidence for multiple losses of photosynthesis in polykrikoid dinoflagellates.
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Single-cell transcriptomics using spliced leader PCR: Evidence for multiple losses of photosynthesis in polykrikoid dinoflagellates.
BMC Genomics. 2015;16:528
Authors: Gavelis GS, White RA, Suttle…
Aug 07
The large mitochondrial genome of Symbiodinium minutum reveals conserved non-coding sequences between dinoflagellates and apicomplexans.
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The large mitochondrial genome of Symbiodinium minutum reveals conserved non-coding sequences between dinoflagellates and apicomplexans.
Genome Biol Evol. 2015 Jul 20;
Authors: Shoguchi E, Shinzato …
Aug 07
Genome sequence of the Roseovarius mucosus type strain (DSM 17069(T)), a bacteriochlorophyll a-containing representative of the marine Roseobacter group isolated from the dinoflagellate Alexandrium ostenfeldii.
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Genome sequence of the Roseovarius mucosus type strain (DSM 17069(T)), a bacteriochlorophyll a-containing representative of the marine Roseobacter group isolated from the dinoflagellate Alexandrium ostenfeldii.
Stand Genomic Sci. 2015;10:17
Authors: Riedel T, Spring S, Fiebig A, Scheuner C, Petersen J, Göker M, Klenk HP
Abstract
Roseovarius mucosus Biebl et al. 2005 is a bacteriochlorophyll a-producing representative of the marine Roseobacter group within the alphaproteobacterial family Rhodobacteraceae, which was isolated from the dinoflagellate Alexandrium ostenfeldii. The marine Roseobacter group was found to be abundant in the ocean and plays an important role for global and biogeochemical processes. Here we describe the features of the R. mucosus strain DFL-24(T) together with its genome sequence and annotation generated from a culture of DSM 17069(T). The 4,247,724 bp containing genome sequence encodes 4,194 protein-coding genes and 57 RNA genes. In addition to the presence of four plasmids, genome analysis revealed the presence of genes associated with host colonization, DMSP utilization, cytotoxins, and quorum sensing that could play a role in the interrelationship of R. mucosus with the dinoflagellate A. ostenfeldii and other marine organisms. Furthermore, the genome encodes genes associated with mixotrophic growth, where both reduced inorganic compounds for lithotrophic growth and a photoheterotrophic lifestyle using light as additional energy source could be used.
PMID: 26203330 [PubMed]
Jul 25
Diversity of Heterotrophic Protists from Extremely Hypersaline Habitats.
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Diversity of Heterotrophic Protists from Extremely Hypersaline Habitats.
Protist. 2015 Jun 18;166(4):422-437
Authors: Park JS, Simpson AG
Abstract
Heterotrophic protists (protozoa) are a diverse but understudied component of the biota of extremely hypersaline environments, with few data on molecular diversity within halophile ‘species’, and almost nothing known of their biogeographic distribution. We have garnered SSU rRNA gene sequences for several clades of halophilic protozoa from enrichments from waters of >12.5% salinity from Australia, North America, and Europe (6 geographic sites, 25 distinct samples). The small stramenopile Halocafeteria was found at all sites, but phylogenies did not show clear geographic clustering. The ciliate Trimyema was recorded from 6 non-European samples. Phylogenies confirmed a monophyletic halophilic Trimyema group that included possible south-eastern Australian, Western Australian and North American clusters. Several halophilic Heterolobosea were detected, demonstrating that Pleurostomum contains at least three relatively distinct clades, and increasing known continental ranges for Tulamoeba peronaphora and Euplaesiobystra hypersalinica. The unclassified flagellate Palustrimonas, found in one Australian sample, proves to be a novel deep-branching alveolate. These results are consistent with a global distribution of halophilic protozoa groups (∼morphospecies), but the Trimyema case suggests that is worth testing whether larger forms exhibit biogeographic phylogenetic substructure. The molecular detection/characterization of halophilic protozoa is still far from complete at the clade level, let alone the ‘species level’.
PMID: 26202993 [PubMed – as supplied by publisher]
Jul 17
Hammondia hammondi harbors functional orthologs of the host-modulating effectors GRA15 and ROP16 but is distinguished from Toxoplasma gondii by a unique transcriptional profile.
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Hammondia hammondi harbors functional orthologs of the host-modulating effectors GRA15 and ROP16 but is distinguished from Toxoplasma gondii by a unique transcriptional profile.
Eukaryot Cell. 2014 Dec;13(12):1507-18
Authors: Walzer KA, Wier GM, Dam RA, Srinivasan AR, Borges AL, English ED, Herrmann DC, Schares G, Dubey JP, Boyle JP
Abstract
Toxoplasma gondii and its nearest extant relative, Hammondia hammondi, are phenotypically distinct despite their remarkable similarity in gene content, synteny, and functionality. To begin to identify genetic differences that might drive distinct infection phenotypes of T. gondii and H. hammondi, in the present study we (i) determined whether two known host-interacting proteins, dense granule protein 15 (GRA15) and rhoptry protein 16 (ROP16), were functionally conserved in H. hammondi and (ii) performed the first comparative transcriptional analysis of H. hammondi and T. gondii sporulated oocysts. We found that GRA15 and ROP16 from H. hammondi (HhGRA15 and HhROP16) modulate the host NF-κB and STAT6 pathways, respectively, when expressed heterologously in T. gondii. We also found the transcriptomes of H. hammondi and T. gondii to be highly distinct. Consistent with the spontaneous conversion of H. hammondi tachyzoites into bradyzoites both in vitro and in vivo, H. hammondi high-abundance transcripts are enriched for genes that are of greater abundance in T. gondii bradyzoites. We also identified genes that are of high transcript abundance in H. hammondi but are poorly expressed in multiple T. gondii life stages, suggesting that these genes are uniquely expressed in H. hammondi. Taken together, these data confirm the functional conservation of known T. gondii virulence effectors in H. hammondi and point to transcriptional differences as a potential source of the phenotypic differences between these species.
PMID: 25280815 [PubMed – indexed for MEDLINE]
Jul 16
Transfer of energy pathway genes in microbial enhanced biological phosphorus removal communities.
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Transfer of energy pathway genes in microbial enhanced biological phosphorus removal communities.
BMC Genomics. 2015;16:526
Authors: Wong DH, Beiko RG
Abstract
BACKGROUND: Lateral gene transfer (LGT) is an important evolutionary process in microbial evolution. In sewage treatment plants, LGT of antibiotic resistance and xenobiotic degradation-related proteins has been suggested, but the role of LGT outside these processes is unknown. Microbial communities involved in Enhanced Biological Phosphorus Removal (EBPR) have been used to treat wastewater in the last 50 years and may provide insights into adaptation to an engineered environment. We introduce two different types of analysis to identify LGT in EBPR sewage communities, based on identifying assembled sequences with more than one strong taxonomic match, and on unusual phylogenetic patterns. We applied these methods to investigate the role of LGT in six energy-related metabolic pathways.
RESULTS: The analyses identified overlapping but non-identical sets of transferred enzymes. All of these were homologous with sequences from known mobile genetic elements, and many were also in close proximity to transposases and integrases in the EBPR data set. The taxonomic method had higher sensitivity than the phylogenetic method, identifying more potential LGTs. Both analyses identified the putative transfer of five enzymes within an Australian community, two in a Danish community, and none in a US-derived culture.
CONCLUSIONS: Our methods were able to identify sequences with unusual phylogenetic or compositional properties as candidate LGT events. The association of these candidates with known mobile elements supports the hypothesis of transfer. The results of our analysis strongly suggest that LGT has influenced the development of functionally important energy-related pathways in EBPR systems, but transfers may be unique to each community due to different operating conditions or taxonomic composition.
PMID: 26173980 [PubMed – in process]
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