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Annotation of microsporidian genomes using transcriptional signals
2012
EA GenoSol CT3; International audience; High-quality annotation of microsporidian genomes is essential for understanding the biological processes that govern the development of these parasites. Here we present an improved structural annotation method using transcriptional DNA signals. We apply this method to re-annotate four previously annotated genomes, which allow us to detect annotation errors and identify a significant number of unpredicted genes. We then annotate the newly sequenced genome of Anncaliia algerae. A comparative genomic analysis of A. algerae permits the identification of not only microsporidian core genes, but also potentially highly expressed genes encoding membrane-asso…
Structural and evolutionary analysis of the copia-like elements in the Arabidopsis thaliana genome.
2001
The analysis of 460 kb of genomic sequence of Arabidopsis thaliana chromosome III allowed us to identify two new transposable elements named AtC1 and AtC2. AtC1 shows identical long terminal repeats (LTRs) and all the structural features characteristic of the copia-like active elements. AtC2 is also a full copia-like element, but a putative stop codon in the open reading frame (ORF) would produce a truncated protein. In order to identify the copia-like fraction of the A. thaliana genome, a careful computer-based analysis of the available sequences (which correspond to 92% of the genome) was performed. Approximately 300 nonredundant copia-like sequences homologous to AtC1 and AtC2 were detec…
Tirant is a new member of the gypsy family of retrotransposons in Drosophila melanogaster.
2000
In this paper, we propose a consensus sequence for a putative complete Tirant retrotransposon. Several defective copies, as well as relevant sequences available in databases have been analyzed. The putative complete Tirant element is 8533 bp long, and presents all the structural features of a retroviruslike transposable element of the gypsy family. It contains three ORFs (open reading frames) that encode putative products resembling the retroviral Gag, Pol, and Env proteins. Southern blot analyses show that complete and defective Tirant elements are widespread in Drosophila melanogaster. The different hybridization patterns observed in several natural populations of this species suggest tha…
bilbo, a non-LTR retrotransposon of Drosophila subobscura: a clue to the evolution of LINE-like elements in Drosophila
1997
We used the repetitive character of transposable elements to isolate a non-LTR retrotransposon in Drosophila subobscura. bilbo, as we have called it, has homology to TRIM and LOA elements. Sequence analysis showed a 5' untranslated region (UTR), an open reading frame (ORF) with no RNA-binding domains, a downstream ORF that had structural homology to that of the I factor, and, finally, a 3' UTR which ended in several 5-nt repeats. The results of our phylogenetic and structural analyses shed light on the evolution of Drosophila non-LTR retrotransposons and support the hypothesis that an ancestor of these elements was structurally complex.
Drosophila melanogaster histone H2B retropseudogene is inserted into a region rich in transposable elements.
1998
We have isolated and characterized the genomic sequence of a Drosophila melanogaster histone H2B pseudogene that is localized outside of the cluster of the replication-dependent histone genes and has all the properties of a retropseudogene. It is highly homologous to the transcribed region of the D. melanogaster histone H2B gene, but not to its flanking regions, and is surrounded by short direct repeats. The pseudogene contains several point mutations that preclude its translation. The sequence of the 3' region of this pseudogene is compatible with the hypothesis that the 3' terminal stem-loop structure of the histone H2B mRNA has served as a primer for the reverse transcription event from …
CCDC 723787: Experimental Crystal Structure Determination
2009
Related Article: D.Mavrynsky, R.Sillanpaa, R.Leino|2009|Organometallics|28|598|doi:10.1021/om8009393
Synergistic Effects of Trichoderma harzianum, 1,3 Dichloropropene and Organic Matter in Controlling the Root-Knot Nematode Meloidogyne incognita on T…
2022
Environmental concerns raised by synthetic nematicides are encouraging integrated management strategies based on their combination with non-chemical control tools, such as biocontrol agents and/or organic amendments. In this study, the combination of the fumigant 1,3-dichloropropene (1,3-D) with a commercial formulation of the biocontrol agent Trichoderma harzianum (TH) and an organic fertilizer (OF) was investigated in two consecutive tomato crops for its effect on the root-knot nematode Meloidogyne incognita and plant growth and yield. The application of 1,3-D was only performed on the first crop, while TH and OF were provided to both crops. Almost all treatments significantly reduced nem…
Fast Poisson solvers for graphics processing units
2013
Two block cyclic reduction linear system solvers are considered and implemented using the OpenCL framework. The topics of interest include a simplified scalar cyclic reduction tridiagonal system solver and the impact of increasing the radix-number of the algorithm. Both implementations are tested for the Poisson problem in two and three dimensions, using a Nvidia GTX 580 series GPU and double precision floating-point arithmetic. The numerical results indicate up to 6-fold speed increase in the case of the two-dimensional problems and up to 3- fold speed increase in the case of the three-dimensional problems when compared to equivalent CPU implementations run on a Intel Core i7 quad-core CPU…
CCDC 922680: Experimental Crystal Structure Determination
2013
Related Article: Ferenc Miklós, István M. Mándity, Reijo Sillanpää, Ferenc Fülöp|2013|Tetrahedron Lett.|54|3769|doi:10.1016/j.tetlet.2013.05.009
Synthesis and reactivity of new mono- and dinuclear niobium and tantalum imido complexes: X-ray crystal structure of [Ta(η5-C5H4SiMe3)Cl2{NC6Me4-4-(N…
2006
Abstract The reaction of [1,4-{SiMe3(H)N}2C6Me4] (1) with 2 equivalents of LiBun followed by the addition of SiMe3Cl gave the diamine compound [1,4-{(SiMe3)2N}2C6Me4] (2). [Ta(η5-C5H4SiMe3)Cl4] reacts with 2, in a 2:1 stoichiometric ratio, to initially yield a mixture of the dinuclear, [{Ta(η5-C5H4SiMe3)Cl2}2(μ-1,4-NC6Me4N)] (3), and mononuclear, [Ta(η5-C5H4SiMe3)Cl2{ NC6Me4-4-(N(SiMe3)2)}] (4), imido complexes. 3 can be obtained exclusively by submitting the reaction mixture to repeated cycles of evacuation, to remove volatiles, followed by addition of solvent and subsequent heating. The mononuclear imido complex 4 was isolated from the reaction of [Ta(η5-C5H4SiMe3)Cl4] with 2 in a 1:1 sto…